Abstract Rapeseed seeding dates are largely delayed under the rice–rape rotation system, but how rapeseeds adapt to the delayed environment remains unclear. Here, five seeding dates (20 October, 30 October, 10 November, 20 November and 30 November, T1 to T5) were set and the dynamic differences between two late-seeding-tolerant (LST) and two late-seeding-sensitive (LSS) rapeseed cultivars were investigated in a field experiment. The growth was significantly repressed and the foldchange (LST/LSS) of yield increased from 1.50-T1 to 2.64-T5 with the delay in seeding. Both LST cultivars showed higher plant coverage than the LSS cultivars according to visible/hyperspectral imaging and the vegetation index acquired from an unmanned aerial vehicle. Fluorescence imaging, DAB and NBT staining showed that the LSS cultivars suffered more stress damage than the LST cultivars. Antioxidant enzymes (SOD, POD, CAT, APX) and osmoregulation substances (proline, soluble sugar, soluble protein) were decreased with the delay in seeding, while the LST cultivar levels were higher than those of the LSS cultivars. A comparative analysis of transcriptomes and metabolomes showed that 55 pathways involving 123 differentially expressed genes (DEGs) and 107 differentially accumulated metabolites (DAMs) participated in late seeding tolerance regulation, while 39 pathways involving 60 DEGs and 68 DAMs were related to sensitivity. Levanbiose, α-isopropylmalate, s-ribosyl-L-homocysteine, lauroyl-CoA and argino-succinate were differentially accumulated in both cultivars, while genes including isocitrate dehydrogenase, pyruvate kinase, phosphoenolpyruvate carboxykinase and newgene_7532 were also largely regulated. This study revealed the dynamic regulation mechanisms of rapeseeds on late seeding conditions, which showed considerable potential for the genetic improvement of rapeseed. Keywords: agronomic characters, multi-omics, oil security, phenylpropanoid biosynthesis, ROS, TCA cycle 1. Introduction Global agriculture production is significantly threatened by changes in the climate and environment, which, without adaptation, are expected to decrease agricultural productivity and raise the risks of crop failure [[42]1,[43]2]. According to existing research, 39% of global crop fields require new varieties to avoid a loss of yield from climate change by the end of the century to ensure food security [[44]3,[45]4]. Asseng et al. (2015) suggested that varieties required more heat units to delay maturity and extend grain development in order to adapt to increased temperatures [[46]5]. According to a case in the Yangtze River Basin (YRB), China, rice–rape rotation is the dominant cropping method; however, farmers have delayed rice harvests to gain a higher yield and grain quality as global warming intensifies, which has led to higher requirements for rapeseed production [[47]6,[48]7]. According to a previous report, as seeding dates are delayed, extreme weather events will occur more frequently, especially when wintering, which will result in widespread reductions in yield and even crop failure [[49]2,[50]8]. Rapeseed (Brassica napus L., AACC, 2n = 38), as an oil crop grown in winter, provides over 47% of the domestic plant edible oil in China. In addition, as rapeseed does not compete with summer staple crops such as rice for land, it is regarded as the most promising winter rotation crop [[51]9,[52]10]. However, as rice harvest time is delayed, the seeding dates of rapeseed will be postponed to as late as December, while its suitable seeding dates are late September to early October [[53]11]. Meanwhile, the maximum air temperature decreases very quickly from near 30 °C in November to even below 5 °C in December, which greatly inhibits the production of rapeseed. As reported, the delay in planting greatly inhibited the photosynthetic rates of rapeseed and led to a dramatic reduction in pod numbers [[54]12,[55]13]. In addition, the oil content has been reported to have reduced by 0.5–1.5% with a one-week delay [[56]14], seriously limiting the production of rapeseed [[57]15]. Therefore, how rapeseed adapts to delayed seeding environment conditions, especially when wintering, has become a vital area of study for future oil security and sustainability. It is worth mentioning that, due to global changes and the low planting enthusiasm of farmers, over 100 million acres of winter fallow fields have been generated in the YRB, of which about 50 million acres can be planted with rapeseed, and if they are fully utilized, over 15.17 million tons of rapeseed oil, which will account for more than 7% of the vegetable oil production of the world, can be produced [[58]16]. Therefore, the adaptation of rapeseed to complex environmental conditions can not only help to improve rapeseed yield, but also benefit the utilization of the large area of winter fallow fields, and hence ensure oil security and sustainability. Among the different adaptation measures in agriculture, variety adaptation has been identified as one of the most effective, and region-specific breeding efforts are needed to achieve an effective adaptation to climate change for sustainability [[59]1,[60]17]. Illustrating the late seeding response mechanisms and breeding tolerance genotypes under late seeding conditions are necessary for food and oil sustainability. Tian et al. (2021) first quantified the extent of winter fallow fields and identified the fallow periods in winter, while assessing the great potential of rapeseed production in the YRB [[61]16]. Luo et al. (2022) provided a more reliable comprehensive index for cold-tolerance evaluation through measurement of the growth parameters during germination and the emergence stage of 436 natural rapeseed populations, based on a pot experiment [[62]10]. In addition, Zhang et al. (2019) evaluated 12 seed-germination- and seedling-emergence-related indices of 132 Brassica napus genotypes under normal and low-temperature conditions and screened out three highly low-temperature-tolerant genotypes [[63]18]. For further illustration, Qin et al. (2023) identified the phenotypic damage and transcriptome profiles of two rapeseed inbred lines in the early flowering stage under cold stress through phytotron experiments, and 1396 DEGs were identified [[64]19]. Similarly, Mehmood et al. (2021) used iTRAQ and transcriptomics to identify 48 DEGs and 17 DEPs corresponding to a cold-tolerant rapeseed line and 82 DEGs and 38 DEPs in a cold-sensitive line at the four-leaf stage in a climate chamber [[65]20]. Furthermore, the effects of antioxidant enzymes, sugar metabolism, the CBF-COR pathway and MAPK signaling on resistance to low-temperature conditions were also identified based on light incubator conditions [[66]21,[67]22]. However, most of these studies were conducted in light incubators, phytotron or climate chambers, which cannot entirely reflect the complex field environment conditions, and contrasting appearances will also occur in field conditions. In addition, late seeding stress contains multiple abiotic and biotic factors, such as cold, chilling, raining, drought and so on, not merely cold or chilling. Against this background, we aimed to identify and characterize the late seeding response mechanisms of rapeseeds (Brassica napus L.) by comparing two late-seeding-tolerant with two late-seeding-sensitive cultivars at five seeding dates. By evaluating their wintering ability according to the measurement of agronomic characters, including multi-spectral, osmoregulation, ROS and antioxidant, the physiological mechanisms were revealed. Furthermore, the interaction analysis of transcriptome × metabolome was also studied, aiming to disclose the adaptation mechanisms of rapeseeds in the YRB under late-seeding-environment conditions. In our view, this is the first study which comprehensively studied the dynamic changes in physiology, genes and metabolites during wintering under field conditions, which will help to identify the merits of late-seeding-tolerant rapeseed and provide fundamental references for future rapeseed breeding.