To optimize the initiation of continuous flow CANON process, the research compared startup course and nitrogen removal performance under distinct NLR in room temperature ((25±1) ℃) between two sets of AUSB reactors, one of which was middle-setting aeration (1#), and the other was bottom-setting aeration (2#). The results showed that 1#, 2# successfully started CANON process treating domestic wastewater with relatively low ammonium concentration (90 mg/L) in 55 d and 70 d respectively. In the progress of increasing nitrogen loading rate gradually, both of them gained the highest nitrogen removal rate, which was 0.280 kg/(m³·d) for 1#, and 0.256 kg/(m³·d) for 2# under the condition of HRT=6 h. In later operation, 1# maintained efficient nitrogen removal status whose eigenvalue (Δρ(TN)/Δρ(NO₃^--N)) remained around 7.83, however, eigenvalue of 2# decreased to 7.49 after 125 d operation owing to the activity of NOB strengthened. The middle-setting aerated AUSB accomplished a higher total nitrogen removal rate which was 74.98% through the combination with simultaneous nitritation-Anammox (SNA) and alternate nitritation-Anammox (ANA) double pathways, which was ascribed to the enhancement of AOB and AnAOB activity and the effective suppression on NOB. Middle-setting aerated AUSB could shorten starting period of continuous flow CANON process, and furthermore realize long-term stable autotrophic nitrogen removal.