Integrated fixed-film activated sludge technology (IFAS) has a great advantage in improving nitrogen removal performance and increasing treatment capacity of municipal wastewater treatment plants with limited land for upgrading and reconstruction. This research aims at investigating the enhancing effects of polyethylene (PE) carrier and nitrifying bacteria PE (NBPE) carrier on nitrogen removal efficiency of an anoxic/aerobic (A/O) system from municipal wastewater and revealing temporal changes in microbial community evolution. A pilot-scale A/O system and a pilot-scale IFAS system were operated for nearly 200 days, respectively. Traditional PE and NBPE carriers were added to the IFAS system at different operating phases. Results showed that the treatment capacity of the IFAS system was enhanced by almost 50% and 100% by coupling the PE carrier and NBPE carrier, respectively. For the PE carrier, nitrifying bacteria abundance was maintained at 7.05%. In contrast, the nitrifying bacteria on the NBPE carrier was enriched from 6.66% to 23.17%, which could improve the nitrogen removal and treating capacity of the IFAS system. Finally, the ammonia efficiency of the IFAS system with NBPE carrier reached 73.0 ± 7.9% under 400% influent shock load and hydraulic retention time of 1.8 h. The study supplies a suitable nitrifying bacteria enrichment method that can be used to help enhance the nitrogen removal performance of municipal wastewater treatment plants. The study’s results advance the understanding of this enrichment method that effectively improves nitrogen removal and anti-resistance shock-load capacity.