In order to further promote the application of mainstream anammox, magnetic field enhancing technology was applied to improve the anammox start-up and operation performance under the conditions of low temperature and substrates concentrations. Two UASBs were adopted as anammox reactors and run in parallel. The controlling group and the magnetic field enhancing group (with 2.4 g/L Fe3O4 NPs) were recorded as UASBC and UASBM. The results showed that UASBC and UASBM successfully took 37 days and 33 days to start mainstream anammox with TNRE of 90.03% and 85.05%, respectively. The maximum TNLR of UASBC and UASBM reached 0.54 mg N(m3·d)−1 and 0.82 mg N(m3·d)−1 with the maximum TNRE of 86.41% and 85.50% during 121 days operation. The results showed that magnetic filed could change morphological characteristics of AnAOB and strengthen sludge granulation by adjusting the composition of EPS. Microbial high-throughput sequencing analysis results showed the phylum of Planctomycetes dominated in UASBC and UASBM with the relative abundance of 26.41% and 32.68% on 121 d. Candidatus Kuenenia was cultured as the dominant bacteria, and it was speculated that magnetic filed had the ability to promoting the enrichment of Candidatus Kuenenia. These findings were interesting and meaningful, and could provide new ideas for long-term application of mainstream anammox.