The deammonification process is a promising and energy efficient nitrogen removal technology. Since deammonification process has succeeded in high-strength ammonia nitrogen wastewater treatment (sidestream deammonification) but its application in treating low-strength ammonium nitrogen wastewater (mainstream deammonification) remains a great challenge. In this study, mainstream deammonification process in two reactors maintained stability with hydrazine (N2H4) addition. The two reactors consisted of a deammonification granular reactor and a mixed ammonia oxidizing bacteria (AOB) flocculent with anaerobic ammonia oxidizing bacteria (AnAOB) granular reactor. Deammonification granular reactor had a more efficient total nitrogen removal efficiency (TNRE, 80.5 ± 5.8%) and nitrogen removal rate (NRR, 0.33 ± 0.04 g/(L·day)). The advantage of retain biomass in granular sludge reactor lead to a more balanced ex-situ activity between AOB (0.37 mg N/(g VSS·h)) and AnAOB (0.43 mg N/(g VSS·h)). Candidatus Brocadia and Nitraspira were detected the dominant genus responsible for the observed AnAOB and nitrite oxidizing bacteria (NOB), respectively. The more obvious effect of N2H4 on enhancing AnAOB and suppressing NOB both in ex-situ activity and genus abundances in mixed sludge reactor were also founded may due to loose spatial distribution among species.