An alternate anaerobic/anoxic–aerobic double membrane bioreactors process (A2N-DMBR) was proposed to improve denitrifying phosphorus removal efficiency. The system was operated for 70 d under different nitrogen/phosphorus (N/P) ratios with synthetic wastewater to present the performance evaluation of nutrients removal and microbial community structure in the A2N-DMBR process. The results showed that when the influent total phosphorus (TP) was 6.4 mg/L, the corresponding N/P ratio of 8.8, the high removal capacity of nitrogen and phosphorus could be achieved with the average effluent TP and total nitrogen (TN) concentration of 0.8 mg/L and 12.0 mg/L, respectively. Periodical test showed that pH and oxidation-reduction potential (ORP) could be used as control parameters for anaerobic phosphate release, and ORP was also closely related with the phosphate uptake in anoxic phase. The high-throughput sequencing analysis revealed that the Proteobacteria and Xanthomonadales-nobank related to biological nitrogen and phosphorus removal was domination bacteria at phylum and genus level in A2N-DMBR system, with the proportion of 42.5% and 39.1%, respectively. Furthermore, Dechloromonas, which was further detected as putative denitrifying phosphorus accumulating organisms (DPAOs), was enriched (9.9%) in the system.