The problem of gas-producing vinegar production seriously troubles production enterprises and causes certain economic losses. In this study, the microorganisms in gas-producing vinegar were isolated and identified, and the main microorganisms and their acid tolerance genes were revealed by metagenomic sequencing technology. Twenty-three bacterial strains were isolated from gas-producing vinegar, all of which were identified as Acetilactobacillus jinshanensise by 16S rDNA. The results showed that the microorganisms in gas-producing vinegar belonged to 24 phyla, 42 classes, 94 orders, 149 families, 233 genus and 450 species, among which the relative abundance of Acetilactobacillus jinshanensise in genera and species levels was greater than 98%, combined with the isolation and identification results of culture medium plate showed that the bacteria was a dominant bacteria in gas-producing vinegar. Egg-NOG database annotated to 2 176 COG functional units, KEGG database annotated to 46 KEGG pathways, CAZy database annotated to 81 carbohydrate active enzymes. The CARD database and VFDB virulence factor data annotations showed that Acetilactobacillus jinshanensise was a safe strain that does not produce toxins. Combined with the sequencing results and database analysis, a total of 13 suspected acid tolerance genes of Acetilactobacillus jinshanensise were screened, involving amino acid metabolism (patA, metE, lysC), cell membrane fatty acid composition (fadB, fadA, fadI), H+-ATPase (capB) and two-component system (luxS). The results provided a reference for elucidating the microbiota and prevention and control provide a theoretical basis of gas-producing vinegar.