The impact of different aeration positions on startup and operation of the continuous flow CANON granular sludge process was considered by inoculating flocculent ANAMMOX activated sludge at room temperature (25±1)℃ in two sets of AUSB reactors. The aeration unit of R1 was installed 0.3 m above the base, while the aeration unit of R2 was set at the bottom. R1 and R2 successfully developed the granule CANON process on the 43rd d and 56th d, respectively. The mean particle diameter of R1 granular sludge increased to 214.79 μm, and the eigenvalue (△NO3--N/△TN) was maintained at 0.128; whereas, the granular sludge size of R2 rose to 205.27 μm with an eigenvalue maintained at 0.129. The nitrogen loading rate (NLR) was gradually increased in the low ammonia-nitrogen (90 mg·L-1) wastewater within R1 and R2. This was more beneficial in R1, resulting in the persistent growth of CANON granular sludge and the enhancement of the systematic nitrogen removal rate (NRR). The average particle diameter of R1 rose to 507.46 μm in 88 d, while NRR reached up to 0.277 kg·(m3·d)-1. R2 granule sludge particle size was 467.72 μm after 108 d of cultivation, and achieved a 0.243 kg·(m3·d)-1NRR, which was 87.73% of that in R1. During the course of steady operation, the specific anoxic/aerobic mode of R1 effectively suppressed NOB microbial activity, the eigenvalue remained around 0.127±0.003, and the NRR of R1 was maintained at about (0.262±0.019) kg·(m3·d)-1. However, NOB was propagated observably in the continuously aerobic R2, whose eigenvalue rose to 0.136±0.004, while NRR was merely (0.231±0.015) kg·(m3·d)-1 after 125 d of long-term operation. During the whole experiment period, the intermediate-setting aerated AUSB accelerated the formation of CANON granular sludge evolving from flocculent ANAMMOX sludge, and better nitrogen removal performance and operational stability were achieved.