Water quality has been greatly confined to the nitrogen loss and phosphorus pollutants caused by agricultural production in the Three Gorges Reservoir Area. This study aims to clarify the characteristics of water quality under different land use types in typical small watersheds. The water quality monitoring was conducted in the Changping small watershed in the Three Gorges Reservoir Area from 2015 to 2020. A systematic investigation was made on the change patterns of Total Nitrogen (TN), nitrate nitrogen (NO3--N), ammonia nitrogen (NH4+-N), Total Phosphorus (TP), Dissolved Total Phosphorus (DTP), and Total Particulate Phosphorus (PP) concentrations in the water bodies under land use types, together with their influencing factors. The results showed that: 1) The overall nitrogen and phosphorus output concentrations of land use types were ranked in the order of the village > sloping farmland > forest land > reservoir. The average TN concentrations were 8.29, 2.88, 1.57, and 1.43 mg/L in the villages, sloping farmland, forest land, and reservoirs, respectively. The average TP concentrations were 0.25, 0.13, 0.09, and 0.07 mg/L, respectively. 2) There was a different water quality of land use types during the flood and non-flood periods. The concentration of nitrogen and phosphorus output in the villages was higher in the non-flood period than that in the flood period. The sloping farmland, forest land, and reservoirs showed a higher concentration in the flood period than those in the non-flood period. 3) The Nemerow comprehensive pollution index demonstrated that the pollution level of both forest land and reservoir was at the clean level, and the sloping farmland was at the light pollution level. But, the pollution level of the village deteriorated from the pollution level to a heavy pollution level, due to the increase in pig farming. 4) The annual output loads of TN and TP in the Changping sub-basin were 4 278.59 and 364.93 kg/a , respectively. Livestock and poultry breeding was the most important source of nitrogen and phosphorus pollution in the sub-basin, with the output loads of TN and TP accounting for 45.69% and 71.77%, respectively. The TN and TP pollution load per unit area of sloping land in the sub-basin were 7.58% and 1.79% of those of village, respectively. The sloping farmland presented significantly low pollution characteristics, compared with the village. Therefore, the sloping farmland can be used to absorb the village sewage and livestock manure, in order to promote the local absorption of manure in the basin for the better effect of multi-source co-management. The land use structure of the whole watershed can also be adjusted in an effective way to control agricultural surface pollution. Therefore, the small watershed was divided into the forest and grass water connotation zone, village pollution control zone, as well as sloping farmland soil and water conservation zone, according to the water quality and ecosystem service function of land use types. Zoning collaborative prevention and control strategy should be an effective way of promoting the water resource, nitrogen and phosphorus transfer from one pollution control zone to another pollution control zone in order to preventing the pollutants export to the out of the small watershed. The finding can provide the theoretical basis and technical support for the control of nitrogen and phosphorus pollution in the protection of water sources in the Three Gorges Reservoir Area.