Pomegranate is sensitive to low temperature, and aril browning is considered as a typical symptom of chilling injury, affecting greatly fruit quality and marketability. A comprehensive comparison of aril traits and secondary metabolites using widely targeted secondary metabolomics was performed between healthy and browning arils. A total of 399 metabolites were identified in arils. Moreover, 75 up-accumulated and 14 down-accumulated were presented in browning arils. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the biosynthesis of plant secondary metabolites related aril browning mainly involved in flavonoid, flavonol, and isoflavonoid, particularly, phenylpropanoid biosynthesis. Additionally, the correlation analysis was carried out between aril traits and weighted gene co-expression network of metabolites. Collectively, aril browning was mainly attributed to water loss, the oxidization of polyphenol oxidase (PPO), and hydrolysis reaction. It was noted that p-coumaric acid may affect greatly pomegranate aril browning. These findings will contribute to elucidating aril browning of pomegranate during cold storage, and developing appropriate postharvest treatments to improve fruit quality.