In this study, nitrifying bacteria were enriched in a membrane bioreactor (MBR, R1) and their bioaugmentation effectiveness was evaluated in another two MBRs (R2 and R3). Nitrifying activated sludge (NAS) with high nitrification activity of up to 3,000 mg-N/(L·d)−1 was successfully enriched in R1. The results showed that chemical oxygen demand concentration of 100–200 mg/L had no negative effect on NAS enrichment but reduced the ratio of bacterial nitrifiers. Moreover, the cell concentration of nitrifying bacteria in NAS, which was 3.1 × 1011 cells/L, was similar to that of the commercial bacterium agent. For the bioaugmentation test, the reactor inoculated with 14% NAS achieved a 23% higher NH4+-N removal efficiency than that of the uninoculated reactor. Along with the improvement of nitrification performance, the bacterial nitrifiers abundance and microbial richness remarkably increased after bioaugmentation. These results suggested that the MBR system could efficiently enrich nitrifying bacteria using organic carbon containing culture medium, and potentially act as a side-stream reactor to enhance the nitrification function of the wastewater treatment plant.