This study aimed to investigate the correlation among the amino acids, fatty acids composition, flavor compounds, and microbial dynamic changes of cured large yellow croaker (Larimichthys crocea) roe (LYCR) with different salt additions (0, 4, 10, 16%, w/w) by the metabolomics and macrogenomics approaches. A total of 22 amino acids, 33 fatty acids, and 57 volatile compounds were detected in cured LYCR. Acinetobacter and Rhodococcus were the dominant genera for 0 and 16% salt-added LYCR, respectively, and Staphylococcus dominated in the 4 and 10% salt-added LYCR. Based on correlation analysis, Staphylococcus was the main influencing factor in the flavor formation of cured LYCR, which was highly associated with fatty acid degradation as well as amino acid degradation pathways, contributing to ester production. These findings were very meaningful for elucidating the flavor formation mechanism, optimizing the curing process, and controlling the product quality of cured fish roe.