Abstract Chinese native pig breeds exhibit unique advantages over Western pig breeds, but the specific lipid metabolism mechanisms remain unclear. The phenotypic characteristics of Mashen (MS) pigs and Duroc × (Landrace × Yorkshire) (DLY) pigs are studied. The results show that MS pigs exhibit higher intramuscular fat (IMF) content. The area of adipocytes of MS pigs is significantly greater than that in DLY pigs (p < 0.01). Lipidomics analysis reveals distinct profiles in the upper layer of backfat (ULB), leaf lard (LL), greater omentum (GOM), and IMF, with MS pigs showing higher polyunsaturated fatty acids (PUFAs) in ULB, LL, and GOM. Key differential lipids identified in the two pig breeds include the following triglycerides (TGs) and phosphatidylcholines (PC): TG(16:1_18:1_18:3), TG(18:1_18:2_18:3), TG(18:3_18:2_18:2), PC(18:0_18:1), and PC(18:0_18:2). Weighted gene co-expression network analysis (WGCNA) reveals lipid molecules associated with serum biochemical indices. Transcriptomics analysis highlights 1944 differentially expressed genes between the MS-ULB and DLY-ULB. Notably, multiple genes from the cytochrome P450 family (CYP2E1, CYP4A24, CYP2J2), along with PLA2G2D, PLA2G4A, and multiple PCs, are associated with the metabolism of arachidonic acids and linoleic acids. PLA2G2D and PLA2G4A are also involved in the metabolism of α-linolenic acids. This comprehensive analysis provides essential information for breeding strategies and meat quality improvement. 1. Introduction Pork is one of the most widely consumed meats globally, significantly impacting human nutrition and culinary traditions [[54]1]. The culinary versatility and nutritional value of pork make it a dietary staple in many regions [[55]2]. Additionally, the production efficiency and quality of pork are closely linked to the production, storage and metabolism of fat [[56]3]. Therefore, a thorough understanding of lipid metabolism in porcine adipose tissue is crucial. Adipose tissue is the most metabolically active energy reservoir in animals [[57]4]. According to the location of fat in pigs, adipose tissue is categorized into subcutaneous adipose tissue (SAT), intramuscular fat (IMF) in skeletal muscle, and visceral adipose tissue (VAT) [[58]5,[59]6]. SAT includes the upper layer of backfat (ULB), inner layer of backfat (ILB), and abdominal subcutaneous adipose (ASA), while VAT comprises the greater omentum (GOM), leaf lard (LL), and other depots [[60]7]. Each fat depot has distinct metabolic properties [[61]8], which affect the overall metabolism through the release of hormones, adipocytokines, and regulatory proteins. These differences contribute to variations in meat quality across different tissues and breeds. While previous studies have predominantly focused on SAT and IMF [[62]9,[63]10], there appears to be metabolic competition between SAT and IMF; reducing SAT while maintaining the optimal IMF level meets the production requirements [[64]11]. The lipid characteristics of VAT and their indirect impacts on meat quality remain unexplored. Our study incorporates the analysis of both LL and GOM. By systematically comparing lipid metabolism across these distinct anatomical depots, including ULB, IMF, LL, and GOM, we provide a comprehensive description of the lipids composition of different tissues. Lipidomics, which involves the comprehensive analysis of lipid composition and metabolism, has a wide range of applications in food science [[65]12,[66]13], nutrition [[67]14], and biomedical research [[68]15,[69]16]. Lipidomics plays a pivotal role in understanding the physiological and biochemical processes that influence meat quality traits [[70]17,[71]18]. For example, meat flavor is a volatile compound produced by the oxidation of lipids, with traditional methods unable to determine the lipid responsible for the desired aroma. Lipidomics, on the other hand, can identify the flavor precursors that have an impact on meat flavor [[72]13]. By identifying and quantifying various lipid species, lipidomics analysis provides valuable insights into the lipid composition of distinct tissues and highlights differential lipid profiles between breeds [[73]19,[74]20,[75]21]. Currently, lipidomics is used to explore various characteristics of pigs. Combining lipidomics with metagenomics has allowed researchers to determine gene characteristics and key markers of lipid deposition across tissues between Lantang and Landrace breeds [[76]22]. Additionally, lipidomics analysis has identified distinct lipid profiles in the livers of Tibetan and Yorkshire pigs [[77]23] and has revealed changes in the fatty acid composition of pig tissues due to different nutrient feedings [[78]24,[79]25]. Local pig breeds often offer unique advantages over commercial breeds, they have better meat quality [[80]26], and superior adaptability to the environment [[81]27]. In this study, lipidomics is used to comprehensively analyze the lipid composition of the native breeds Mashen (MS) pigs and Duroc × (Landrace × Yorkshire) (DLY) pigs from the perspective of lipid metabolism for the first time, filling the gap of lipidomics in the field of livestock genetic resources, and providing a basis for the improvement of lipid characteristics of native pigs. DLY pigs are a widely used crossbreed, known for its faster growth rate but poorer fat storage capacity [[82]28]. On the other hand, MS pigs usually have a lower final weight, but higher backfat thickness and leaf fat content [[83]29]. Given that body weight serves as a critical production indicator in livestock husbandry, and our primary focus lies in production performance, we conduct comparative analyses of adipose tissues between MS and DLY pigs at comparable body weights. However, there is a significant difference in growth rate between the two pig breeds. In order to reach the same body weight as DLY pigs, MS pigs require a longer time. This may cause differences in lipid deposition due to changes in the epigenetic modifications of genes [[84]30]. In this study, the types and abundances of lipids are identified through lipidomics. The receiver operating characteristic (ROC) and weighted gene co-expression network analysis (WGCNA) are used to identify key lipids. Additionally, transcriptomic analysis reveals differential gene expression patterns in subcutaneous fat, providing insights into the variations in lipid metabolism between the two breeds. The integration of lipidomic and transcriptomic data facilitates the identification of interacting lipids and genes, elucidating the complex interplay between genetic and metabolic factors influencing meat quality traits. This study aims to elucidate the unique lipid metabolism mechanisms underlying the superior meat quality traits of MS pigs compared to the commercial DLY pigs, with a focus on identifying breed-specific lipid profiles, key regulatory genes, and molecular pathways that drive differences in fatty acid composition. These results are crucial for developing breeding strategies and producing pork products that align with consumer preferences and nutritional needs.