The responses of total nitrogen (TN) and total phosphorus (TP) removal performance and microbial community to 0-1.2 g/L FeO@SiO nanoparticles (NPs) in sequencing batch reactors were investigated. Results showed that an appropriate dose of FeO@SiO NPs (0.3 g/L) could promote the removal efficiency of TN and TP. High-throughput sequencing results indicated that microbial richness increased, whereas microbial diversity did not vary upon exposure to 0.1-1.2 g/L FeO@SiO NPs. The relative abundances of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria increased from 11.75%, 3.52%, and 6.77%, respectively, at 0 g/L FeO@SiO to 27.05%, 7.21%, and 14.77%, respectively, upon exposure to 0.3 g/L FeO@SiO. At the genus level, 0.3 g/L FeO@SiO NPs enriched norank_f_Nitrosomonadaceae, norank_f_Xanthomonadaceae, Amaricoccus, and Shinella. Real-time quantitative polymerase chain reaction results suggested that the gene copy number of ammonium-oxidizing, nitrite-oxidizing, and denitrifying bacteria population remarkably increased, whereas the number of phosphorus-accumulating organisms slightly increased under long-term exposure to 0.3 g/L FeO@SiO NPs. Energy-dispersive spectrum analysis showed that the phosphorus content was higher at 0.3 g/L FeO@SiO than at 0 g/L FeO@SiO. Nitrogen removal primarily occurred through a biological mechanism, while most phosphorus in wastewater may be removed by the combination of physicochemical and biological methods.