The application of low-salt fish sauce is limited by its tendency to spoil easily and inadequate flavor generation. Herein, a salt-tolerant Tetragenococcus halophilus 2MH-3 strain with strong abilities of enzyme production and biogenic amine degradation was utilized as a starter for the production of low-salt fish sauce. Bacterial community analysis revealed discrepancies in microbiota between low-salt fish sauces fermented with (Th group) or without 2MH-3 (LF group). Staphylococcus was the primary genus in the Th group at 1 M fermentation (47.42 %), followed by Psychrobacter (10.82 %), while Tetragenococcus swiftly ascended to the dominant status with a relative abundance of 5.88 % after 3 M fermentation. Conversely, the abundance of Tetragenococcus throughout the LF fermentation period was no significant change. In Th group, 118 volatile components were detected with 21 high-concentration flavor compounds being the primary flavor components (OAV ≥ 1), which were basically produced by Alkaliphilus, Psychrobacter, Tetragenococcus, Bacteroides and Staphylococcus based on the co-occurrence heatmaps after PLS-DA evaluation. Furthermore, the co-occurrence network map demonstrated that the decrease in key biogenic amines such as histamine, putrescine, cadaverine and tyramine, the increase in bacterial diversity, as well as the increase in 21 core volatile flavor compounds (OVA ≥ 1.0), were mainly caused by the addition of T. halophilus 2MH-3 in the low-salt fish sauce. Therefore, T. halophilus 2MH-3 could be utilized as an underlying microbial starter in the industrialization of fish sauce.