Recently, a flocculent-granular hybrid reactor was reported as a novel nitrogen removal system; however, the mechanisms of stable operation in the system remain unclear. In this study, the mechanisms of the stable nitrogen removal performance in a flocculent-granular hybrid system were investigated with temperature reduction. The operational period was divided into three phases with different temperatures ranges. In phase I, the nitrogen removal efficiency was stabilized at about 90% with nitrogen removal load maintained at approximately 0.28 kg N/(m3·day). In phase II, while decreasing the temperature to 20 °C, the activities of key enzymes were reduced immediately and were then maintained at a certain level. The relative abundances of aerobic ammonium-oxidizing bacteria and anaerobic ammonium-oxidizing bacteria gradually increased at this phase. In phase III, after the temperature dropped to 15 °C, the activities of key enzymes gradually increased due to adaptation to low temperature, boosting the nitrogen removal efficiency to 83%.