Abstract Microbial fermentation can be responsible for flavor production and increasing the nutritional quality of fermented fish foods. The study aimed to isolate non-halophilic bacteria possessing proteolysis and lipolysis properties as starter cultures for low-salt content fermentation of coarse fish. The strains with high enzyme activities were screened and multiple growth characteristics were analyzed. The content of amino acid nitrogen and trichloroacetic acid (TCA)-soluble peptides in fermented fish was also investigated under different fermentation conditions. Nuclear magnetic resonance (NMR) metabolomics analysis was utilized to monitor the metabolite profile of fermented fish paste. The isolate was identified as Bacillus velezensis DZ11. The strain DZ11 exhibited obvious hydrolysis properties of lipids and proteins. During the fermentation of fish paste, a total of 40 differential metabolites were identified, of which multiple metabolites changed significantly, including nutrient-related substances and flavor precursors. Salt concentration and strain DZ11 had important effects on the differential metabolites. B. velezensis DZ11 under longer fermentation time promoted the formation of flavor precursors and potentially increased the nutritional substances of low-salt fermented fish.