This study investigated the performance of full nitration-denitration (FND) and partial nitration-denitration-anammox (PNDA) in treating a synthetic wastewater with 300 mg/L NH4+-N and 600 mg/L COD. It was found that approximately 40% higher total nitrogen removal was achieved via PNDA than via FND. Meanwhile, high-throughput sequencing also revealed that aerobic heterotrophic bacteria were predominant in the FND process, while facultative and even anaerobic bacteria including anammox bacteria were dominant in PNDA process. Furthermore, the mass balance on nitrogen showed that 44% of nitrogen was removed by partial nitration-denitration, while 36% via nitritation-anammox pathway in the PNDA process, with the significant saving in aeration and demand of organic carbon source. Compared to the FND process, it is obvious that the PNDA process will offer a more cost-effective alternative with easy operation for treating ammonium-rich organic wastewater.