The partial nitrification (PN) performance and the microbial community variations were evaluated in a sequencing batch reactor (SBR) for 172 days, with the stepwise elevation of ammonium concentration. Free ammonia (FA) and low dissolved oxygen inhibition of nitrite-oxidized bacteria (NOB) were used to achieve nitritation in the SBR. During the 172 days operation, the nitrogen loading rate of the SBR was finally raised to 3.6 kg N/m/d corresponding the influent ammonium of 1500 mg/L, with the ammonium removal efficiency and nitrite accumulation rate were 94.12% and 83.54%, respectively, indicating that the syntrophic inhibition of FA and low dissolved oxygen contributed substantially to the stable nitrite accumulation. The results of the 16S rRNA high-throughput sequencing revealed that Nitrospira, the only nitrite-oxidizing bacteria in the system, were successively inhibited and eliminated, and the SBR reactor was dominated finally by Nitrosomonas, the ammonium-oxidizing bacteria, which had a relative abundance of 83%, indicating that the Nitrosomonas played the primary roles on the establishment and maintaining of nitritation. Followed by Nitrosomonas, Anaerolineae (7.02%) and Saprospira (1.86%) were the other mainly genera in the biomass.