As one of the four major staple crops, potato exhibits significant differences among varieties. Therefore, understanding the relationship between nutritional quality and molecular metabolism in potato varieties is essential for facilitating the development of the processing industry and improving dietary nutrition. In this study, six potato varieties: Mincaishu 1 (C1), Mincaishu 2 (C2), Mincaishu 3 (C3), Mincaishu 4 (C4), Minshu 2 (M2), and Minshu 3 (M3) were tested for metabolomics and transcriptomics analyses. The aim of this study was to investigate the molecular basis underlying the formation of distinctive traits in these varieties. The two varieties with the greatest differences in metabolites were C4 and C1, exhibiting disparities in 657 substances. These differential substances were primarily involved in metabolic pathways such as the synthesis and degradation of ketone bodies, the citrate cycle (TCA cycle), and alanine, aspartate, and glutamate metabolism. Further transcriptomic analysis revealed that the overall gene expression level in stems was lower than in leaves for all six varieties. However, the expression patterns of the same genes were consistent between leaves and stems across different varieties. The highest number of differentially expressed genes was observed in the leaves of C4 and C1. Additionally, through a correlation analysis of transcriptomic and metabolomic data, this study identified several shared pathways between the two omics approaches, including the citrate cycle and sulfur relay system metabolism. This study will serve as a cornerstone for advancing potato breeding and agricultural practices by improving yield, quality, and the metabolic profile of important potato traits, with our multi-omics analysis providing crucial insights into potato metabolism and facilitating the exploration of innovative breeding strategies.