The effects of influent shift from synthetic wastewater to anaerobically pretreated actual sewage coupling with lowering temperature on microbial community of a two-stage partial nitritation (PN)-anammox process were evaluated through high-throughput sequencing. Venn diagrams and Hill numbers showed the significantly increased bacterial diversity both in the PN and anammox reactor. However, taxonomic analysis indicated that outstanding enrichment of heterotrophic bacteria and reduction of autotrophic species mainly occurred in the PN reactor, while nearly all of the dominant bacteria in the anammox reactor only slightly decreased in abundance. Moreover, immigrant bacteria from the PN reactor to the following anammox reactor had no negative effect on the anammox function. These results implied the positive role of the first-stage PN in maintaining the stability of the following anammox community. Nitrosomonas europaea (17.9-52.9%) and one cluster (19.2-27.7%) within Candidatus Brocadia remained as the dominant functional species in the PN and anammox reactor, respectively.