An integrated process consisting of an anaerobic/anoxic expanded granular sludge bed (EGSB) reactor and an aerobic sequencing batch reactor (SBR) was developed by a mode of sequencing batch operation, in which methanogenesis, denitrification and anammox were coupled in EGSB with methanogenesis first, then denitrification and anammox simultaneously, and partial nitrification occurred in SBR for providing nitrite to EGSB. This process extended the application of the anammox process to the treatment of wastewater containing high concentrations of chemical oxygen demand (COD) and ammonium. When the volumetric exchange ratio between EGSB and SBR was controlled at 57% with the influent pH at 6–8, 74.38–83.65% of NH4+-N, 72.68–83.12% of total nitrogen (TN) and 88.34–98.86% of COD were removed in a range of 200–4,500 mg/L COD and 40–90 mg/L NH4+-N respectively. TN removal by anammox and shortcut denitrification was 26.35–58.64 and 0–32.80% of the removed nitrogen, respectively. The results showed that the contribution of anammox gradually decreased with an increase in the C/N ratio of influent, whereas the reverse was true for shortcut denitrification. The COD removal by methanogenesis was 70.89–98.79% of the removed COD, and increased with increasing C/N ratio.