Wastewater treatment plants (WWTPs) face great challenges in developing countries, such as China, due to increasingly strict integrated wastewater discharge standard, especially for ammonium. Thus, it is very important to understand the limiting factor for ammonium removal in WWTPs. In this study, samples from 8 full-scale municipal WWTPs with different treatment processes in Pearl River Delta (PRD) area were evaluated. Bacterial and archaeal communities were investigated by high-throughput sequencing, activity of aerobic ammonium and nitrite oxidation, denitrification and anammox processes were evaluated. Nitrite, nitrate and TP concentration were strongly correlated with bacterial and archaeal composition in WWTPs based on canonical correspondence analysis (CCA). Aerobic ammonium... oxidation activities were over 10 times lower than aerobic nitrite oxidation, denitrification and anammox activities in WWTPs samples, which indicated nitrogen removal activities in WWTPs were limited by aerobic ammonium oxidation, because of lack of nitrite/nitrate for denitrification and anammox. Moreover, a technology-dependent shaping of microbial diversity and nitrogen removal activity was observed. The highest bacterial diversity and nitrogen removal activities were achieved in sequencing batch reactor (SBR) and Modified Anaerobic-Anoxic-Oxic (MAAO) processes, which implied the advantage of these two treatment technologies in nitrogen removal. Therefore,this study suggested enhancing activity of aerobic ammonium oxidation might be a potential solution, for promoting ammonium removal and benefiting sustainable management of WWTPs in future.