To explore the underlying mechanisms affecting differences in color quality across various parts of yak meat, the chuck, short loin, and sirloin parts were selected to determine their lightness (L*), redness (a*), and yellowness (b*) values. Differentially expressed proteins (DEPs) from different yak meat parts were extracted and identified. Pearson’s analysis was used to examine correlations between the relative quantitative values of DEPs and a*, b*, and L* values. Significant DEPs for meat color were screened and subjected to GO functional annotation and KEGG pathway analysis. Results showed that among the 88 DEPs identified, 20 were significantly correlated with meat color and exhibited different degrees of regulatory effects. Biological information analysis indicated that the color quality of different yak meat parts was affected by 26 biological functions, mainly including carbon metabolism, protein binding, and other molecular functions. Additionally, the 20 significant DEPs were involved in 48 metabolic pathways, mainly including metabolism, glycolysis/glycogenesis, protein processing in the endoplasmic reticulum, and carbon metabolism. PPI network analysis of the DEPs demonstrated that heat shock proteins, the myosin heavy chain, and hemoglobin subunits were key proteins that influenced variations in the color quality of different yak meat parts. This study demonstrates that yak meat color exhibits significant variability across different parts, with the differential expression of proteins exerting significant effects on color quality, thereby providing new theoretical data for further research on proteins related to the color of different yak meat parts and the mechanisms underlying their formation.