Ecological control of non-point source in small watershed is an important means to control agricultural non-point source. Qianjiagou, which is a typical small watershed in Danjiangkou reservoir area, was selected as the object, and the effect of non-point source ecological resistance control system was evaluated by monitoring the water quality at the outlet of the small watershed, monitoring the inflow and outflow water of each control measures, and calculating pollutant load reduction. The results showed that after the ecological resistance control system of Qianjiagou was stable for half a year, the TN, NO₃-N, NH₃-N, COD_Mn and TP in the outflow of the small watershed decreased by 38%, 23%, 63%, 49% and 16%, respectively. Among the resistance control measures, surface flow wetland had higher removal rates of NH₃-N (54%), TP (70%) and TSS (78%), the ecological pond and ecological ditch had higher removal rates of TN (36%, 39%), NO₃-N (43%, 37%) and COD_Mn (63%, 56%), the small artificial wetland had higher removal rates of TN (56%), NH₃-N(85%), COD_Mn (84%), TP(57%) and TSS(87%) and the ecological filter wall had higher removal rate of TSS (81%). The overall reduction rates of COD_Mn, NH₃-N, TN and TP loads by the resistance control system were 56%, 73%, 63% and 59%, respectively.