In this study, the characteristics partial nitrifying biomass in the Sequencing Batch Reactor (SBR) for aerobic granulation was investigated based on experiments and simulation modeling. The reactor operation was carried out at high concentration of ammonium (200~850 mg N/L) which favored Ammonia-Oxidizing Bacteria (AOB) growth over Nitrite-Oxidizing Bacteria (NOB) growth. In partial nitrifying granulation, both Free Ammonia (FA) and Free Nitrous Acid (FNA) simultaneously influenced the activity of NOB much more than that of AOB. According to the simulation results, thE Dissolved Oxygen (DO) concentration and oxygen affinity affect the growth competition and can influence the species that are predominant in the reactor. Both AOB and NOB can have growth potential under toxicants (FA and FNA) inhibition and limited oxygen condition. The AOB growth forms inner part of granule's biofilm, but the NOB growth does not engage in the formation of granules.