According to the characteristics of traditional freshwater ponds in aquaculture, a system of ecological engineering water recirculation ponds aquaculture was designed to solve the problems of aquatic pollution, waste of water and the safety of aquatic product. The system was composed of an eco-ditch, an eco-pond, constructed underflow wetlands and aquaculture ponds, with the area ratio of 1:5:3:30. In the system, the aquaculture ponds were arranged in series, and water flow facilities were built in the pond diagonal to exchange the upper and lower layer water. An impetus was used to circulate the water in the system. At the fish density of 0.20–0.82 kg/m3 and daily water exchange rate of 10%–15% in the system, the concentrations of ammonia nitrogen, nitrite nitrogen, nitrate nitrogen, total nitrogen, total phosphorus and CODMn were lower than 1.89, 0.20, 1.50, 3.27, 0.59, and 9.0 mg/L, respectively, which were all lower than those of the control pond and satisfied the standards of national aquaculture water quality. The water purification results of ecological engineering facilities showed that, the removal rates of total nitrogen, total phosphorus and CODMn from the aquaculture emissions were above 52%, 39% and 17%, respectively, in the constructed underflow wetlands. The average removal rates of total nitrogen, total phosphorus and CODMn were above 18.35%, 17.39% and 18.18%, respectively, in the ecological ditch. And the average removal rates of total nitrogen, total phosphorus and CODMn were 24.72%, 26.32% and 5.86%, respectively, in the eco-pond. Compared to the traditional pond aquaculture, the ecological engineering water recirculation ponds aquaculture system can save as much as 63.6% water and reduce 81.9% COD emissions, which show significant effects on water saving and pollution emission reducing.