There is a problem of flatulence in the production of modern chili sauce. Previous studies have shown that it was mainly caused by bacteria. To further clarify the source of the gas production in chili sauce, the traditional culture medium and 16S rDNA sequencing were used to analyze the species and content of the bacteria from the chili sauce production equipment and the air of the workshop. The MRS and LB mediums were used to isolate six aerobic bacteria and sixteen anaerobes from above samplings. The aerobic bacterial density in the air of raw material storehouse, frying room, and packaging room is 3.0×102, 1.3×104, 8.2×102 CFU/m3 respectively, while the anaerobic bacteria density is 1.4×103,3.4×103,7.0×101 CFU/m3 respectively. The aerobic bacterial density in the equipments of raw material storehouse, frying room, and packaging room is 1.4×105,7.6×105,3.6×107 CFU/g respectively, while the anaerobic bacteria density is 2.1×105, 8.7×105, 7.4×107 CFU/g respectively. By 16S rDNA sequencing, genus Bacillus was dominant in each section. In three production sections, the proportion of Bacillus was 52.31%, 80.23%, 100.00% respectively, while in anaerobic bacteria, the percentage of Bacillus was 28.69%, 80.23%, 65.00% respectively. Based on the species and the total number of bacteria, it was concluded that the traditional heating sterilization could not efficiently kill the Bacillus, and the packaging line had the risk of pollution hazards.