Long period start-up is one of the main restraining factors of the single-stage completely autotrophic nitrogen removal over nitrite (CANON) process. This study investigated the fast start-up of the CANON process initiated by a submerged biological aerated filter (SBAF) method. With conventional activated sludge from the secondary sedimentation tank of municipal waste water treatment plants as the seed sludge, the CANON process was successfully started up after the acclimation of sludge microorganisms for 48 days under the experimental conditions of (30±2)℃,organic carbon free and controlled dissolved oxygen(stage I:0.3-0.5mg•L -1 ; stage II-IV:0.1-0.2mg•L -1 ), with the maximum removal ratio of ammonia nitrogen and total nitrogen achieved at 99.9% and 86.5%, respectively. The population structure characteristics of microorganisms in the system were studied by using high-throughput sequencing of 16SrDNA amplicon. The results demonstrated that the two dominantmicrobial strains in the system were Proteobacteria and Planctomycetes, accounting for 26.6% and 17.8%, respectively. The major contributors of nitrogen removal were Nitrosomonas in β-Proteobacteria and Candidatus brocadia in Brocadiae. Through above experiments, it was revealed that the investigated SBAF based CANON possesses the advantages of fast start-up, efficient nitrogen removal biologically and stable operation process.