The existence of perfluorooctane sulfonate (PFOS) in large quantities threatens environment biosafety. However, the fate of PFOS in a sequencing batch reactor (SBR) system and its influence in system has not yet been revealed. In this study, the fate and behavior of PFOS in an SBR processing system were investigated. Mass balance analyses revealed that PFOS removal was mainly through adsorption. After the reactors were run for 20 days, the PFOS (100 mg/L) removal rate was only 28%. Under the influence of PFOS, the removal rates of chemical oxygen demand (COD) and ammonia nitrogen dropped rapidly from 92, 98% to 23, 35% in the 20th day of system operation, respectively, while, accumulation of nitrite and nitrate was reduced. Compared with the control group, PFOS stimulates microorganisms to secrete more soluble microbial products (SMP) and extracellular polymeric substances (EPS). The adsorption of PFOS and EPS causes sludge bulking and decreases settling. The richness and diversity of microorganisms decreased significantly, affecting the system's removal of COD and ammonia nitrogen. Therefore, the SBR system is not suitable for treating wastewater containing PFOS. It is necessary to remove PFOS through pretreatment to reduce its impact on the SBR system. © 2021 Elsevier Ltd