The performance of simultaneous carbon (C), nitrogen (N) and phosphorus (P) removal was investigated by altering the cycle times in an anaerobic-aerobic-anoxic sequencing batch reactor (AOA-SBR) system. Results showed that the AOA-SBR system achieved high simultaneous C, N and P removal efficiency with a cycle time of 6 h, with average removal efficiencies for COD, TN, and TP of 96.81%, 96.32% and 94.33%, respectively. The highest anoxic removal rate of NO-N was 203.44 mg·g- MLVSS·d. Meanwhile, anaerobic release rate and aerobic, anoxic removal rate of TP reached peak values of 104.31 and 85.81 mg·g- MLVSS·d, respectively. Microbial community analysis demonstrated that Proteobacteria, Bacteroidetes and Candidatus Saccharibacteria at phylum level and Betaproteobacteria, Gammaproteobacteria, Sphingobacteriia, Deltaproteobacteria and Alphaproteobacteria at the class level benefited AOA-SBR performance. Functional analysis of genes indicated that the metabolic potential related to C, N and P metabolism increased under the optimal cycle time condition.