Abstract Background Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic. Colored maize is rich in nutrients, which have received attention for their role in diet-related chronic diseases and have different degrees of anti-stress protection for animal and human health. Methods A comprehensive metabolome (LC-MS/MS) and transcriptome analysis was performed in this study to compare different colored maize varieties from the perspective of multiple recombination in order to study the nutritional value of maize with different colors and the molecular mechanism of color formation. Results Maize kernels with diverse colors contain different types of health-promoting compounds, highlighting that different maize varieties can be used as functional foods according to human needs. Among them, red-purple and purple-black maize contain more flavonoids than white and yellow kernels. Purple-black kernels have a high content of amino acids and nucleotides, while red-purple kernels significantly accumulate sugar alcohols and lipids. Conclusion Our study can provide insights for improving people’s diets and provide a theoretical basis for the study of food structure for chronic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-023-09272-x. Keywords: Maize, Metabolomics, Kernel color, Nutritional quality, RNA-seq Background Maize, or corn (Zea mays L.) is one of the most important cereal crops in the world [[43]1]. Color formation is an important part of maize kernel development, and yellow kernels are the dominant maize planted in the world [[44]2]. Colored maize has received attention due to its role in diet-related chronic diseases [[45]3]. Therefore, the market has different positioning demands for different colors of maize, which can be processed into different products [[46]4]. Preferences for