In application of anammox process, the operation of the conventional expanded granular sludge bed reactor (EGSB) is severely limited by the blocking and decay of floating anammox granules.To address this emerging issue, a novel three-phase separator configuration was designed and an anammox granules circulating EGSB (EGSB) was proposed in this study. In the EGSB, an influent scour on floating granules, whose effect was confirmed by simulation with a three-dimensional flow model, was obtained by integrating the external three-phase separator with the influent and the external cycle. After 166-d operation, the nitrogen removal efficiency of the EGSB reached 75.6%, being 1.28-times that of the EGSB (58.9%). The sludge concentration in the main body of the EGSB reached 3112 ± 65 mg/L, compared with 2613 ± 42 mg/L in the EGSB (p < 0.05). Moreover, the severe granules blockage and decay problem that is frequently encountered in the EGSB no longer occurred in the EGSB. The relative abundance of anammox bacteria in granules from the three-phase separator of the EGSB was 29.7%, significantly higher than that from the EGSB (16.1%, p < 0.05). The blockage and decay of granules in the three-phase separator of the EGSB led to an obvious proliferation of heterotrophic bacteria, with their relative abundance increased by 9.4% compared with the seed sludge (38.6% vs. 29.2%). This study proposed a practical three-phase separator configuration to sustain efficient and stable operation of anammox processes toward the promotion of granules circulation, retention and reaction.