Granular deammonification process is a good way to retain aerobic and anaerobic ammonia oxidizing bacteria (AOB and anammox bacteria) and exhaust flocculent nitrite oxidizing bacteria (NOB). In this study, to facilitate indigenous AOB growth on anammox granules, by stepwise reducing influent nitrite, anammox granules were effectively transformed into deammonification granules in a micro-aerobic EGSB in 100 days. Total nitrogen removal efficiency of 90% and nitrogen removal rate of 2.3 g N/L/d were reached at stable deammonification stage. High influent FA and limited oxygen supply contributed suppression for Nitrospira-like NOB. In transition stages, Proteobacteria and Chloroflexi were always dominated. Anammox abundance decreased, while AOB abundance grew fast. Anammox bacteria and AOB were dominated by Brocadia fulgida and Nitrosomonas europaea, respectively. Denitrification activity and bacteria existed although without influent organic. The final AOB abundance was about 4.55-13.8 times more than anammox bacteria abundance, with almost equal potential activities.