[Objective] The effect of carbon source regulation (cyclic carbon source addition) to induce PAOs’ extensive P-release on characteristics of the microbial in a continuous anaerobic/aerobic alternating biological filter (AABF) operated for phosphorus (P) removal and accumulation was investigated. [Methods] Intracellular storage polymer dyeing, scanning electron microscopy (SEM) and restriction enzyme analysis technology of polymorphism (RFLP) were employed to characterize the changes of microbial communities in biofilm before and after the terminal carbon source regulation in the AABF’s long-term operation. [Results] During carbon source regulation period, the amount of big coccus and cocco-bacillus microbes decreased and the filamentous microbes increased instead in AABF after carbon source regulation; bacterial diversity reduced greatly, the predominance of β-proteobacteria increasing from 56.9% to 72.5%. [Conclusion] Terminal carbon source addition (induce P-release/P-recovery of operation) with corresponding dosage regulation could cause great changes in microbial morphologies and the dominate bacteria ratio increased rapidly. The results of the study provide informative reference on improving the efficiency of biological phosphorus removal system with process control.