A recovery reregulation was adopted for a completely autotrophic nitrogen removal over nitrite (CANON) system, for which the shortcut nitrification process deteriorated. The evolution of the microbial construct was evaluated by 16S rDNA sequencing technology during the recovery regulation period, paying special attention to nitrifiers and anammox bacteria. The high concentration of NH₄⁺-N (over 300mg/L) and extending the ratio of aeration/non-aeration to 1:3could effectively inhibit nitrite-oxidizing bacteria (NOB). In the later period of the stable phases, the nitrite-oxidizing rate (NOR) and ΔNO₃^--N/ΔNH₄⁺-N decreased to 2.30g N/(m³·h) and 0.13respectively; while, the total nitrogen removal rate (TNRR) gradually increased to 0.35kg N/(m³·d). Then, extending the non-aeration time to 90min reduced NOR to nearly zero. The results of 16S rDNA gene high-throughput sequencing indicated that the relative abundance of Nitrospira, the major bacteria of NOB, decreased from 3.96% to 0.64%, and the relative abundance of Candidatus_Jettenia, the major bacteria of anaerobic ammonia-oxidizing bacteria (AnAOB), increased to 49.98% from 46.68%. Our findings elucidated that increasing the influent concentration of ammonia nitrogen can inhibit and eliminate NOB effectively, making AnAOB get enrichment and favoring CANON system recovery.