A continuous flow reactor (CFR) and a sequencing batch reactor (SBR) were operated in parallel to investigate the difference between anammox granulation in CFR and SBR under decreasing temperature and no strict anaerobic condition. The results showed that the biomass achieved initial granulation successfully (D [4, 3] = 280.44 and 346.28 μm) in both CFR and SBR on day 70. Compared with SBR, a better performance (0.33 kg N m−3 d−1) was gotten in CFR due to a better retention capacity of biomass (1397 mg L−1), when seasonal drop of water temperature occurred (18–14 °C). Thus, different operations led to different granulation styles of anammox. Granules in CFR had better rheological properties than that in SBR. Based on a stable and suitable environment provided by CFR, anaerobic ammonium oxidation bacteria (AnAOB) are able to self-aggregate easily and secret extracellular polymeric substances (EPS), which can capture other bacteria as home guardians. In SBR, AnAOB live inside the tan granules under the protection of other bacteria and thick EPS; other aggregations stick to solid carrier surface to form biofilm.