Use of low-salt fish sauce (Yulu) is limited due to its perishable property and rapid loss of unique flavor. In this study, a salt-tolerant strain, Bacillus subtilis B-2, with high protease production was used as a microbial starter for low-salt Yulu fermentation. A total of 133 volatile compounds were detected through HS-SPME-GC-MS. Most aldehydes, alcohols, ketones, furans, and hydrocarbons reached their maximum at 15 d, while most esters, aromatic compounds, acids, nitrogen compounds, and sulfur compounds peaked at 45 d. The 16S rRNA gene high-throughput sequencing showed that Bacillus remained in high abundance during fermentation, reaching 93.63% at 45 d. The characteristic volatile flavor was obviously improved while the microbial contamination was significantly reduced in low-salt Yulu fermented with B. subtilis, compared with those without a microbial starter. The correlation network map suggested that the significant decrease in Pseudomonas, Achromobacter, Stenotrophomonas, Cyanobium, Rhodococcus, Brucella, Tetragenococcus, and Chloroplast contributed most to the decreasing richness and evenness of the microbial community, while Bacillus was the only genus playing a key role in the inhibition of spoilage microorganisms and improvement of volatile flavor after B. subtilis addition. This study suggests the potential use of salt-tolerant B. subtilis as a special starter for industrial Yulu fermentation in the future.