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• The CANON reactor transformed from flocs-granules hybrid to granule-based system. • Nitrogen removal performance was better in flocs-granules hybrid system. • The nitrogen removal pathways of the different systems were calculated. • The distribution and bioactivity of function bacteria were analyzed. Flocs and granules tend to coexist in a single reactor. Granules can improve microbial retention capacity, however, the role of flocs in the CANON reactor remains unclear. The changes in the nitrogen removal performance and microbial communities between flocs-granules hybrid and granule-based systems were studied in this experiment. With a reduction in the flocs ratio (35% → 10%), the nitrogen removal performance deteriorated. The average nitrogen removal efficiency and rate dropped from 81.4% to 67.2% and from 0.225 to 0.174 kg/(m3·d), respectively. The contribution of heterotrophic denitrifying bacteria decreased from 13.5% to 1%, leading to changes in the nitrogen removal pathways between the systems. Furthermore, the activities of anaerobic and aerobic ammonium oxidizing bacteria declined dramatically, which weakened the nitrogen removal performance. Thus, the hybrid system with a flocs ratio near 35% is recommended for use in a CANON reactor. [ABSTRACT FROM AUTHOR]