The sterilization effect of soy sauce under different conditions were studied, the optimal parameter is 130 ℃ maintained 15 s. Tracking and analyzing the degree of pollution with each process of sterilization- filling and diatomite, the result showed that the aerobic and anaerobic viable count of the sterilized sauce reached its peak after adding the diatomite in the frame filtering process, the total number of bacteria are 4.9×10³ CFU/mL and 3.1×10³ CFU/mL respectively, the diatomite is the contamination source and the filtration process is the main contamination point. Separation of contamination microbes in diatomite and finished deterioration sauce, analyzing theirs 16S rDNA sequence, they are identified as Bacillus licheniformis, Bacillus megaterium, Bacillus halodurans, that cause the finished sauce deterioration. These strains also appeared in the sample of diatomite, further evidenced the diatomite is the main contamination source. Base on this, the soy sauce manufacturers are suggested strengthening the microbial testing of diatomite, replacing diatomite frame filter with membrane filtration, preventing the deterioration of finished sauce caused by microbial contamination.