Abstract: Moving bed biofilm reactor (MBBR) was used to treat simulated wastewater. The effect of ammonia-nitrogen concentration (20, 30, 50, 100, 200 mg/L) on the treatment efficiency of MBBR was investigated. By using 16S rDNA high-throughput sequencing technique, the changes in the microbial community structure of MBBR under different ammonia-nitrogen concentration were analyzed. The results indicated that the lower ammonia-nitrogen concentration, the more beneficial for the removal of ammonia nitrogen, but the less impact on the removal of COD, when ammonia-nitrogen concentration was 30~100 mg/L. When ammonia-nitrogen concentration was 20, 50 and 200 mg/L, Ottowia was the top dominant bacterial genus, whose relative abundances were 66.76%, 34.40%, 53.88%, respectively. When ammonia-nitrogen concentration was 30, 100 mg/L, Ottowia was replaced by Arcobacter, Hydrogenophag, etc. The fluctuation of microbial community structure may be related to the competition for dominant position between various denitrifying bacteria and Ottowia. The relative abundance of autotrophic nitrification bacteria was stable at about 0.3%, which was not affected by ammonia nitrogen concentration. The inhibiting effect of high concentration ammonia nitrogen on nitrifying bacteria might be due to the inhibition of their microbial activity. The influent ammonia-nitrogen concentration affected the microbial community structure in MBBR biofilm.