Aiming at the effect of aerobic starvation environment on the nitrification and phosphorus removal performance of activated sludge and the variations of the microbial community evolution during long-term aerobic starvation periods, an activated sludge with high level removal (>99%) of ammonium and phosphorus was used to study the differences of microbial community structures by Illumina high-throughput sequencing technology during 3,7, 14, and 30 d aerobic starvation periods. Results showed that the performance of nitrification and phosphorus removal decreased with the increase of the aerobic starvation time, and the change of microbial community structure was more obvious with the proceeding of aerobic starvation. During short-term (7 d) aerobic starvation period, the functional bacteria including nitrifiers and phosphorus removing bacteria utilized the released ammonium from cell decay and intracellular storage polymers for cell maintenance to guarantee the recovery of nitrification and phosphorus removal performance. Besides, higher activity resuscitation rate of ammonium oxidizing bacteria (AOB) than nitrite oxidizing bacteria (NOB) contributed to the shift of the nitrification pathway from nitratation to nitritation. Furthermore, the abundances of functional bacteria gradually decreased with the prolonging of aerobic starvation time. The microbial community structures of the activated sludge underwent a dynamic change during the 30 d aerobic starvation period, in which the majority of the original dominant species within the phylum Proteobacteria and Bacteroidetes declined with a remarkable increase of Firmicutes that could acclimatize themselves to the aerobic starvation conditions.