Abstract: Ecological branch and purification pond are the end link of control technology system of agricultural non-point source pollution in South China water network area. The study on the allocation scale of ecological branch and purification pond corresponding to farmland area has not been determined yet. In Nanjing Taihe rice production cooperative, ecological branch and purification pond have been constructed at the end of the small watershed hydrological pathway. 4 sampling sites was set along the direction of the water flow in the ecological branch and purification pond. Annual water samplings at the 4 sites were carried out and the concentrations of TN, NH₄⁺-N, TP, and COD were monitored. Annual purification efficiency of the ecological branch and purification pond were analyzed, and the allocation scale of ecological branch and purification pond corresponding to unit farmland area were discussed. The results showed the average total removal rates of TN, NH₄⁺-N, TP and COD in the ecological branch and purification pond were respectively 40.1%，46.8%，27.3% and 35.6%。In the rice season, the total removal rates of TN, TP and COD in ecological branch and purification pond were significantly higher than those in the vegetable season. Under low temperature conditions in winter, the concentrations of TN, TP, and COD at the outlet of the purification pond were still lower than those at the inlet of it. To estimate the allocation scale of ecological ponds based on the loss of nitrogen and phosphorus from farmland and the removal efficiency of ecological branch and purification pond, the area ratio of farmland to ecological ponds is approximately from 23∶1 to 29∶1. To estimate the allocation scale of ecological ponds based on runoff volume from farmland, the area ratio of farmland to ecological ponds is approximately from 21∶1 to 33∶1. To avoid affecting the runoff discharge of small watersheds during the rainy season, the measure of storing muddy water and releasing clear water should be used and the high-concentration runoff at the beginning of rainfall should be stored in the ecological ponds for treatment.