To compare microbial community structure, diversity and metabolic potential, and analyze their relationships with the spoilage characteristic between Scomber japonicus and Larimichthys crocea, Illumina MiSeq sequencing technology was used to sequence the 16S rRNA V3-V4 hypervariable region of bacteria, and the physicochemical and microbiological indices including pH, total volatile basic nitrogen (TVB-N), histamine and aerobic plate count (APC) were detected. The correlation between microbes and fish spoilage and histamine producing was investigated by Pearson analysis, and the relationship between bacterial community composition and metabolic function was also predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). The results showed that the pH, TVB-N, histamine content and APC in both fish fillets increased with the storage time extention, however their values in S. japonicus fillet increased faster and kept higher than those in L. crocea throughout storage. TVB-N and histamine content reached 76.34 mg/100 g, 59.92 mg/100 g in S. japonicus, while 59.98 mg/100 g, 3.11 mg/100 g in L. crocea at the end of storage, respectively. An increase tendency was observed in richness and diversity of bacteria in S. japonicus muscle and then followed by a decrease during the storage, while a sustained increase tendency was observed in that of L. crocea. Shewanella was the dominant bacteria in fillets of both S. japonicus and L. crocea. Twelve types of bacteria in S. japonicus were screened as TVB-N correlation bacteria, ten of which also showed significant correlation with the histamine producing, meanwhile seven types of bacteria in L. crocea were screened as TVB-N correlation bacteria, however, no bacterium showed correlation with histamine producing. Amino acid metabolism and carbohydrate metabolism were higher than other metabolism during the storage. The abundance of function genes related to amino acids metabolism and carbohydrate metabolism in S. japonicus was enormously higher than that in L. crocea throughout the storage period such as histidine, arginine and proline metabolism and butanoate metabolism, propanoate metabolism and pyruvate metabolism, respectively. This may partially explain why S. japonicus was more perishable than L. crocea from the level of metabolism of the bacterial community. Our study provided a new method to understand the spoilage characteristics of different aquatic products from the perspective of bacterial community and their metabolism related function genes.