Constructed wetlands (CWs) have been successfully employed to treat domestic sewage, while it is reported that inconsistent and low nutrient removal efficiency has been achieved. Due to the good performance in other treatment systems, magnetic Fe3O4 nanoparticles (Fe3O4 NPs) can provide a new pathway for the nutrient removal in CWs. In this study, the influences of Fe3O4 NPs on the nutrient removal and variation of microbial community were investigated. The CWs with Fe3O4 had better NH4<sup>+</sup>-N (ammonia nitrogen, 95.9%), NO3<sup>-</sup>-N (nitrate nitrogen, 83.8%), and TP (total phosphorus, 90.4%) removal percentages than that without Fe3O4. High-throughput sequencing analysis indicated that the microbial community structure could be changed by Fe3O4 NPs. For example, at class level, the major bacteria such as Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were promoted by Fe3O4 NPs. On the other hand, at genus level, some abundant genera disappeared, while other abundant genera became dominant in CWs with Fe3O4 NPs, including Desulfuromonas (3.0%), Azospirillum (1.9%), Chryseolinea (1.5%), and Desulfomicrobium (1.8%). The latter genera essentially improved the microbial community involved in the nitrogen removal. Therefore, the CWs with Fe3O4 NPs showed higher NH4<sup>+</sup>-N and NO3<sup>-</sup>-N removal percentages than that without Fe3O4 NPs.