The assessment of spatial and temporal variation of water quality influenced by land use is necessary to manage the environment sustainably in basin scales. Understanding the correlations between land use and different formats of nonpoint source nutrients pollutants is a priority in order to assess pollutants loading and predicting the impact on surface water quality. Forest, upland, paddy field, and pasture are the dominant land use in the study area, and their land use pattern status has direct connection with nonpoint source (NPS) pollutant loading. In this study, two land use scenarios (1995 and 2010) were used to evaluate the impact of land use changes on NPS pollutants loading in basins upstream of Three Gorges Reservoir (TGR), using a calibrated and validated version of the soil and water assessment tool (SWAT) model. The Pengxi River is one of the largest tributaries of the Yangtze River upstream of the TGR, and the study area included the basins of the Dong and Puli Rivers, two major tributaries of the Pengxi River. The results indicated that the calibrated SWAT model could successfully reproduce the loading of NPS pollutants in the basins of the Dong and Puli Rivers. During the 16-year study period, the land use changed markedly with obvious increase of water body and construction. Average distance was used to measure relative distribution patterns of land use types to basin outlets. Forest was mainly distributed in upstream areas whereas other land use types, in particular, water bodies and construction areas were mainly distributed in downstream areas. The precipitation showed a non-significant influence on NPS pollutants loading; to the contrary, interaction between precipitation and land use were significant sources of variation. The different types of land use change were sensitive to NPS pollutants as well as land use pattern. The influence of background value of soil nutrient on NPS pollutants loading was evaluated in upland and paddy field. It was found that total nitrogen (TN) and total phosphorous (TP) in upland were more sensitive to NPS pollutants loading than in paddy fields. The results of this study have implications for management of the TGR to reduce the loading of NPS pollutants into downstream water bodies.