The novel partial nitrification endogenous denitrification and phosphorus removal (PNEDPR) process can achieve deep-level nutrient removal from low carbon/nitrogen municipal wastewater without extra carbons. However, its performance is limited by long hydraulic retention time (HRT) and low specific endogenous denitrification rate (r(NO2)). This study aimed at investigating the effects of two improving strategies on PNEDPR. One was decreasing both anaerobic and anoxic reaction time for shortening HRT from 55 h to 17.5 h. The other was temporarily discharging orthophosphate-rich supernatant for balancing the competition between phosphorus and glycogen accumulating organisms to further raise r(NO2) without deterioration of phosphorus removal. Results revealed that, desirable nutrient removal was obtained, as average effluent concentrations of total nitrogen and orthophosphate were 8.4 and 0.5 mg/L with their average removal efficiencies of 86.8% and 90.9%. High-throughput sequencing analysis revealed that, Candidatus_Competibacter conducted nitrogen removal endogenous denitrification and Candidatus_Accumulibacter and Tetrasphaera ensured phosphorus removal.