To study the impact of ammonia nitrogen concentration on the CANON process in different sludge systems, the nitrogen removal performance was researched by the sudden decrease of the influent ammonia concentration in the stable operation of the granule and combined floc-granule CANON process at the temperature of (30±1) ℃ and the pH of 7-8. Under the conditions of FA concentrations at 34, 20 and 10 mg/L, the short cut nitrification of the granule system was stable, and the ratio of nitrate increase/ammonia consumption was less than 0.11. When the FA concentration was 33 mg/L, the short cut nitrification operated stably in the combined floc-granule CANON system. When the concentration of FA was decreased to 16 mg/L, the ratio of nitrate increase/ammonia consumption was close to 0.11 and the NOB activity was recovered slightly. When the concentration of FA was decreased to 7 mg/L, the ratio of nitrate increase/ammonia consumption reached to 0.37 and the NOB activity was fully recovered. The results show that the granular sludge system has better resistance to shock loads compared to the combined floc-granule system, and the shorter settling time is the key to ensure the stable operation of granular sludge system. After the partial nitrification was destroyed, the activity of NOB was effectively inhibited by increasing ammonia concentration. The distribution rule of sludge size can be used to determine the stability of the reaction system, and the nitrogen removal performance of CANON process in this study. The quantitative PCR results show that, the abundance of ANAMMOX has obvious decreasing when the ammonia concentration decreased, and the abundance of NOB has obvious growth with the granules disaggregation.