Ethyl carbamate (EC) is a carcinogen that detected in fermented foods. Development of strategies for reducing EC content in fermented foods is the priority to improve the safety of fermented foods. Bacillus amyloliquefaciens JP21, a strain could reduce both EC and urea, was isolated from fermented grains for making Luzhou-flavour Baijiu by high-throughput screening. Enhancement of B. amyloliquefaciens JP21 during Luzhou-flavour Baijiu fermentation reduced EC and urea in fermented grains by 17% and 12%, respectively. The results also showed that addition of B. amyloliquefaciens JP21 presented no effect or had no effect on the flavor of Luzhou-flavour Baijiu. Enzymes used to degrade EC and urea from B. amyloliquefaciens JP21 was partial purified. The optimal pH and temperature for this enzyme to catalyze degradation of urea and EC was detected to be 5.5 and 35 ℃, respectively. It also showed tolerance to low concentration of ethanol. This study adopted the endogenous microbial intervention method to reduce ammonia (amine) toxic compounds in a complex microbial community.