In this study, three sequential batch biofilm reactors (SBBRs) were operated for 155 days to evaluate the performance of completely autotrophic nitrogen removal over nitrite (CANON) process under different aeration modes and dissolved oxygen (DO). Synthetic wastewater with 160-mg NH4 ⁺-N/L was fed into the reactors. In the continuously-aerated reactor, the efficiency of the ammonium nitrogen conversion and total nitrogen (TN) removal reached 80% and 70%, respectively, with DO between 0.8–1.0 mg/L. Whereas in the intermittently-aerated reactor, at the aeration/non-aeration ratio of 1.0, ammonium was always under the detection limit and 86% of TN was removed with DO between 2.0–2.5 mg/L during the aeration time. Results show that CANON could be achieved in both continuous and intermittent aeration pattern. However, to achieve the same nitrogen removal efficiency, the DO needed in the intermittently-aerated sequential batch biofilm reactor (SBBR) during the aeration period was higher than that in the continuously-aerated SBBR. In addition, the DO in the CANON system should be adjusted to the aeration mode, and low DO was not a prerequisite to CANON process.