A laboratory-scale sequencing airlift bioreactor continuously treating high-level 4-chloroaniline (4-ClA) wastewater was used for studying the effect of 4-ClA on the characteristics and microbial community of aerobic granular sludge. The granulation of aerobic sludge and efficient pollutant removal performance were developed via shortening sludge settling time and gradually increasing influent 4-ClA concentration to around 400 mg L−1. However, the granular sludge reactor deteriorated with the 4-ClA loading rate above 0.8 kg m−3 d−1. Denaturing gradient gel electrophoresis and real-time quantitative PCR were applied to investigate the microbial community succession during the start-up and recovery of bioreactor. The results showed that the performance of granular reactor was significantly influenced by the microbial community of aerobic granule, and stable aerobic granule was dominated with β-Proteobacteria (61.28 %), Flavobacteriales, Planctomycetales, Clostridiales, and Acidobacteria. Since Thauera (21.55 %) related to the genus β-Proteobacteria was abundant in the stable 4-ClA-degrading granular sludge, it was speculated as the main 4-ClA-degrading bacteria. Under high chloroaniline level, the sludge granulation may maintain the stability of the bioreactor via adjusting the composition of microbial community and abundance of functional microorganism. This paper provided useful information for better understanding the change of microbial community characteristics under high-level toxic organic pollutants and process optimizing.