A system for treating ammonia-based wastewater is provided. The system includes a first reactor, including: denitrification bacteria for denitrification; a second reactor disposed on the back of the first reactor, wherein the second reactor includes an aerator and aerobic heterotrophic bacteria, and has an HRT of less than 6 hours; a third reactor disposed on the back of the first reactor, wherein the third reactor contains nitrification bacteria carried on the carriers for improving nitrification; and a solid-liquid-separating reactor disposed on the back of the third for separating the solids and liquids in the effluent of the third reactor.