In the operation of completely autotrophic nitrogen removal over nitrite (CANON) process, a recently developed new type of nitrogen removal, the improper control of DO can easily lead to the decline or even collapse of the nitrogen removal rate. The key to the stable operation of the CANON process is reasonable control of dissolved oxygen inside the reactor. Given controversies of the present findings on the startup and long running of CANON in different aeration modes, the startup and performance of CANON process were tested in SBR with two different aeration strategies—intermittent aeration (R1) and the continuous aeration (R2).Results showed that the CANON was successfully developed in both R1and R2 within 21 d and 27 d. After extended aeration damage, CANON of R1and R2 fully recovered within 25 d and 33 d on conditions of HRT change and run cycle increase. The final TN removal rates of R1 and R2 were 84.32% and 73.62%.The results further showed that both alternating nitritation/anammox and simultaneous nitritation/anammox contributed to N-removal in SBR, and their contributions in R1 accounted for 58.54% and 24.7% (86 d). The bioactivity of ammonia oxidizing bacteria (AOB) and anaerobic ammonia oxidizing bacteria (AnAOB) in R1 was higher than that of R2, while the bioactivity of nitrite oxidizing bacteria (NOB) showed a contrary result. Intermittent aeration is an effective means to obtain stably high TN removal.