The effects of polyether sulfone (PES) microplastic concentration on the nitrifying process of aerobic granular sludge (AGS) were investigated together with the microbial community structure of AGS. The PES microplastic concentration inhibited the removal of ammonia nitrogen only to a small extent. The average total nitrogen removal rate increased by 5.6% after PES addition. On the 30th day, the addition of 0.5 g/L PES inhibited the specific nitrate reduction rate (SNRR) by 38.84 mg N/(g MLSS·h). Nitrite oxidase (NOR) performance of the AGS were inhibited with addition the PES. According to the high-throughput sequencing results, in the presence of PES, the abundance of Bacillales_Incertae Sedis XII reduced, while the abundance of Anaerolineaceaen increased in the AGS. According to the clusters of orthologous groups (COG) and kyoto encyclopedia of genes and genomes (KEGG), the content of cytochrome c-containing reduced and the Amino Acid Metabolism increased with addition 0.5 g/L PES microplastic.