Stable and efficient partial nitrification reaction and nitrite accumulation are essential for the operation of partial nitrification-anaerobic ammonia oxidation process. This paper investigated the changes in the performance of a partial nitrification bioreactor during the domestication process. After 40 days of domestication, the partial nitrification reaction remained stable, the nitrite accumulation rate (NAR) increased significantly to 85.7%, and the NO2 --N/NH4 +-N ratio stabilized at 1.25 ± 0.04. Both diversity indices (Simpson and Shannon) and richness indices (Ace and Chao1) tend to decrease with domestication. Nitrosomonas as a typical ammonia oxidizing bacterium it increased its relative abundance in the reactor from 0.02 ± 0.007% at P1 to 11.6 ± 2.2% at P2, and at P3 stage the denitrifying functional bacteria norank_f_AKYH76, Dokdonella and unclassified_f_Comamonadaceae reached 33.4 ± 12.5%, 18.8 ± 1.8%, and 10.1 ± 1.3%, respectively, and the increase in the relative abundance of these functional species was also consistent with the accumulation of nitrite nitrogen in the reactor.