Microplastic polyamide 66 (PA66) was used to explore its mechanism of influence on the contaminants removal from aerobic granular sludge (AGS) and the corresponding change to the microbial community. Results showed that the removal pollution efficiency of the experimental groups with PA66 were inhibited during the early treatment stage. However, as the experiment progressed, the removal efficiencies of chemical oxygen demand (COD) (92.66%, 93.10%, 93.11%, 93.79%) and ammonia nitrogen (94.25%, 94.58%, 95.61%, 94.73%) were similar in the addition 0 g/L (A), 0.1 g/L (B), 0.2 g/L (C) and 0.5 g/L (D) PA66 beakers at the last 10 days. On the first day, the intensity of fluorescence peaks representing tryptophan protein-like and aromatic protein-like substances of loosely-bound extracellular polymeric substances (LB-EPS) indicated that the PA66 microplastic caused damage to the sludge structure, and the intensity of fluorescence peaks representing fulvic acid-like and humic acid-like substances were stronger than those in the control beaker (A). Microbial community analysis showed that the main phyla were Firmicutes (49.11%, 59.77%, 44.33%, 41.21%), Proteobacteria (26.44%, 11.96%, 31.44%, 19.4%) and Bacteroidetes (9.24%, 13.05%, 11.89%, 14.71%) in the four beakers. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, genes representing [T] Signal transduction mechanisms illustrated that adding PA66 microplastic resulted in more signaling molecules in the AGS.