In this study, we investigated the dynamic changes in muscle lipid content (MLC) deposition in the breast muscle of Jingyuan chickens at different stages (42-, 126-, and 180- days old) using metabolomics. The pH_45min, a*, and L* were significantly increased in the breast muscle of 126-day-old chickens, and MLC and b* were significantly increased in the breast muscle of 180-day-old chickens. A total of 4643 differentially expressed metabolites (DEMs) were identified, of which 10 decreased and 29 increased with age. Key pathways associated with meat quality traits included oxidative phosphorylation, β-alanine metabolism, and glycerophospholipid metabolism. Combined transcriptomic and phenotypic correlation analyses revealed significant positive correlations of MLC, pH_45min, a*, and L* with LysoPC 20:4, CD3E, TARP, IL7R, ENSGALG00010025331, and RASSF5. In the 42- and 180-day-old chickens, MLC, pH_45min, a*, and L* were significantly and positively correlated with L-Anserine, Dihydroxyacetone phosphate, ENSGALG00010006904, and HSPB7. MLC, pH_45min, a*, and L* were significantly and positively correlated with beta-Nicotinamide adenine dinucleotide in the 126- and 180-day-old chickens. This study deepens our understanding of the differences in MLC deposition at different stages of Jingyuan chickens and its relationship with meat quality traits.