The widespread use of graphene oxide (GO) raises environmental concerns. Municipal wastewater treatment systems are potential receptors of GO containing streams, yet the influences of chronic toxicity of GO on these systems are poorly understood. In the present study, the responses of nutrient removal performance and microbial community to long-term GO exposure were investigated. The results showed that reduction in performance of COD, ammonia and phosphate removals was observed during the whole experiment. The highest effluent COD contents 56.07 mg/L occurred when influent GO concentration was 30 mg/L. Low concentration of GO (1-10 mg/L) had a greater impact on ammonia and phosphate removal performance, the highest effluent concentration of ammonia and phosphate was 9.51 mg/L and 2.72 mg/L. However, there was a certain recovery trend of removal efficiency in each concentration gradient. The results of 16S rRNA gene sequencing showed that long-term GO exposure significantly altered the composition and structure of activated sludge microbial communities. Specifically, both bacterial richness and evenness indexes decreased as the GO concentration increased. Significant shift of bacterial community structures was observed after GO addition and then recover slightly at recovery stage without GO addition. Moreover, functional bacteria, such as Dechloromonas, Nitrosomonas, Nitrospira, Defluviicoccus, and Chryseobacterium were significantly shifted, which may be associated with altered nutrient removal performances and EPS production. And protein content in EPS varied between 103.54 mg/L and 206.84 mg/L. The findings in this study provide new insights into our understanding of the potential effects of long-term GO exposure on wastewater treatment systems.