This study assessed the toxic effects of bisphenol A (BPA) on the microbial community and the function of activated sludge in sequencing batch reactors (SBRs). The toxicity of BPA was mitigated through dosing sludge with Rhodococcus Req-001. BPA reduced the biomass of sludge, and the proportion of viable bacteria decreased with the aggravation of BPA pollution. BPA affected the secretion of extracellular polymeric substances (EPSs), increased the ratio of polysaccharide to protein, and deteriorated the sedimentation performance of sludge. BPA decreased the abundances of functional bacteria involved in the degradation of organic matter and water purification, including Polaromonas, Dechloromonas, and Nitrospira, and the water purification capacity of the reactor decreased. Req-001 enhanced the BPA removal efficiency by 15%, and increased ammonia nitrogen and phosphorus removal by 8.8% and 22.7%, respectively. The functional recovery ability of the sludge system and the high removal ability of Req-001 make it a promising specie for use in BPA bioremediation. This study combined the effect of BPA on activated sludge and reactor performance with the microbial community, clarified the toxic mechanism of BPA on activated sludge, and therefore provides a theoretical basis and potential solutions to help WWTPs cope with the toxic effects of BPA.