Hexanal contributes significantly to meat flavor. The aim of this study was to identify the metabolic pathways of hexanal formation in chicken meat. We found 32 metabolites associated with hexanal content in chicken meat, mainly including fatty acids (linoleic acid, etc., positive correlation) and some amino acids (L-proline, etc., negative correlation). A comparative analysis of the expression of these 32 metabolites between two groups of chickens with high- and low-hexanal content revealed that L-proline and phenylacetaldehyde were downregulated, while ADP-ribose and 4-methylphenol were upregulated in the high-hexanal content chickens. It was also found that the increase of ADP-ribose induced the conversion of L-proline to other amino acids, such as arginine, through a process likely involving the pyrimidine metabolism pathway, leading to a reduction in proline content, which in turn abolished the inhibitory effect of proline on hexanal and enhanced the formation of hexanal. These findings confirm the effect of linoleic acid on hexanal content, and also reveal a negative regulatory effect of proline on the production of hexanal and its elimination mechanism in chicken meat.