For the stable operation of simultaneous nitrification-endogenous denitrification and phosphorus removal (SNEDPR) system under domestic sewage, sequencing batch reactor (SBR) was selected to inoculate SNEDPR granular sludge under artificial water distribution. The actual domestic sewage and sludge were pretreated by mixed hydrolysis acidification and taken as the influent matrix, and the stable operation of the system was realized by optimizing the pretreatment unit hydraulic retention time (HRT) combined with SBR sludge discharge modes. Results showed that when the HRT of the pretreatment unit decreased from 12 h to 4 h, the content of acetic acid, propionic acid, and the proportion of volatile fatty acids (VFA) provided by the hydrolytic acidification solution increased, the anaerobic poly-hydroxyalkanoate (PHA) storage in aerobic granular sludge (AGS) increased, the simultaneous nitrification and denitrification (SND) efficiency increased to 58.1%, and the effluent TN decreased to about 7.8 mg/L. At the same time, under bottom sludge discharge, the proportion of small particles in SBR increased, LB-EPS increased, and the settlement performance of the system became worse. The proportion of mature and aged large particles under top sludge discharge increased, and the moisture content and strength of particles decreased. Under selective sludge discharge, the particle size in SBR was concentrated in 0.5-0.9 mm, with dense particle structure and high strength. The layered distribution of bacteria in the particles enhanced the SND effect. Batch experiments showed that the activities of nitrite-oxidizing bacteria (NOB) and glycogen accumulating organisms (GAOs) were reduced, the proportion of denitrifying polyphosphate accumulating organisms (DPAOs) with NO-₂ as electron receptor in the system was increased to 40.5%, and the efficiency of simultaneous nitrification and endogenous denitrification phosphorus removal was improved. The short HRT combined with selective sludge discharge of the pretreatment unit had stable performance in the treatment of domestic sewage particles. The effluent TN and TP met the first-level A standard specified in GB 18918—2002 Discharge Standard of Pollutants for Municipal Wastewater Treatment Plant. The system can achieve efficient and stable removal of nitrogen and phosphorus.