Agricultural drainage is one of the leading contributors to agricultural non-point source (AGNPS) pollution in China. It is difficult to treat due to its dispersed nature. In recent years, although agricultural drainage water has been reused in agricultural production, its poor quality has limited its potential utilization. To optimize its reuse, we designed and tested a treatment system for agricultural-drained water compromising a vegetation buffer, slopes (plant filter), a water collection area, and a soil-retention wall in Hengxi town, Nanjing, Jiangsu Province, China. By exploiting the soil-vegetation buffer strips, nitrogen and phosphorus in the paddy field’s surface drainage are expected to be reduced dramatically. Test results suggest that after applying basal fertilizer, the removal rates of total nitrogen by the soil-vegetation buffer strips are 90.6% and 95.2% for controlled and conventional irrigation-drainage treatments, respectively. In addition, the removal rates of dissolved nitrogen are 92% and 90.7% (controlled and conventional), the removal rates of total phosphorus are 94.2% and 92.9%, and for dissolved phosphorus, the rates are 94.4% and 95%, respectively. These data indicate that drainage water from a paddy field that has been treated through the constructed system could reach the standard of National Class II with two irrigation-drainage methods, while for control treatments water quality can only reach Class V, which is severely contaminated. With this system, the reuse of agricultural water resources could be achieved, which will undoubtedly provide a great potential for agricultural water management in southern China, as well as achieving excellent overall ecological benefits.