The effects of CeO2 nanoparticles (CeO2 NPs) on a sequencing batch biofilm reactor (SBBR) with established biological phosphorus (P) removal were investigated from the processes of anaerobic P release and aerobic P uptake. At low concentration (0.1 mg/L), no significant impact was observed on total phosphorus (TP) removal after operating for 8 h. However, at a concentration of 20 mg/L, TP removal efficiency decreased from 83.68% to 55.88% and 16.76% when the CeO2 NPs were added at the beginning of the anaerobic and aerobic periods, respectively. Further studies illustrated that the inhibition of the specific P release rate was caused by the reversible states of Ce3+ and Ce4+, which inhibited the activity of exopolyphosphatase (PPX) and transformation of poly-β-hydoxyalkanoates (PHA) and glycogen, as well as the uptake of volatile fatty acids (VFAs). The decrease in the specific P uptake rate was mainly attributed to the significantly suppressed energy generation and decreased abundance of Burkholderia caused by excess reactive oxygen species. The removal of chemical oxygen demand (COD) was not influenced by CeO2 NPs under aerobic conditions, due to the increased abundance of Acetobacter and Acidocella after exposure. The inhibitory effects of CeO2 NPs with molecular oxygen were reduced after anaerobic exposure due to the enhanced particle size and the presence of Ce3+.