In the fierce market competition, high-quality chicken products often stand out. There are significant differences in meat quality between yellow and white feathered chickens. However, the underlying mechanisms that lead to the differences in their meat quality remain unclear. Single nucleotide polymorphisms (SNP) are effective molecular markers that can be utilized in marker-assisted breeding programs targeting chicken meat quality traits. Our research findings indicated that the bloodline of yellow-feathered chickens can significantly alter the meat quality traits of chickens, especially in terms of the shear force and meat color of the breast muscle. Additionally, through metabolomic, lipidomic, and RNA-seq, we identified differentially expressed metabolites, lipids, and genes that influence meat quality. Furthermore, we discovered a key gene, the purinergic receptor P2 × 5 (P2RX5), which significantly contributes to meat quality traits. We identified five SNP sites within the P2RX5 gene and conducted genotyping. Three of these SNP sites were found to be significantly associated with meat quality traits in chickens, such as the a*value and cooking loss. These results indicated that our findings provide potential molecular markers for changing meat quality traits in chickens. However, due to our small sample size and the absence of testing on males, the generalizability of the results may be insufficient.