The bioactivity and biodiversity of nitrite-oxidizing bacteria (NOB) in completely autotrophic nitrogen removal over nitrite (CANON) process should be suppressed to ensure stable operation. In this study, five membrane bioreactors (MBR) were operated as CANON process with different COD concentration, to investigate the influence on NOB structure. The five MBRs were seeded with same sludge and operated under totally same condition, while the influent C/N ratio was set as 0, 0.5, 1.0, 2.0 and 4.0, respectively. Results revealed that the low COD addition performed effective inhibition on NOB, the bioactivity and biodiversity of Nitrobacter and Nitrospira both decreased with the COD increasing when C/N ratio was lower than 1.0. However, massive COD addition (C/N ratio higher than 1.0) resulted in nitrite accumulation in CANON reactors, which then enhanced the NOB. It was concluded that the influent C/N ratio should be controlled around 1.0, to suppress NOB and ensure the stability.