Stable performance is a technical problem in the completely autotrophic nitrogen removal over nitrite (CANON) process with one single stage, which needs to be addressed. In the current work, a laboratory-scale submerged aerated biological filter (SABF) with a 3-L working volume was introduced into the CANON process to enhance its stable performance for 290 days under the following conditions: temperature of 30 ± 1 °C and dissolved oxygen (DO) level of 0.2–0.8 mg·L−1. The results showed that the average ammonium nitrogen removal efficiencies (ANRE) and total nitrogen removal efficiencies (TNRE) were 97.4% and 75.7%, respectively. A 16S rRNA gene high-throughput sequencing technology confirmed the phyla Proteobacteria and Planctomycetes as the ammonium oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AnAOB) of this CANON process with SABF, respectively. The major contributor to nitrogen removal was the genus Candidatus Brocadia, in Brocadiae. The aim is to present an effective strategy as a reference for the design of full-scale plant for the CANON process.