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Land use/cover change (LUCC) affects canopy interception, soil infiltration, land-surface evapotranspiration (ET), and other hydrological parameters during rainfall, which in turn affects the hydrological regimes and runoff mechanisms of river basins. Physically based distributed (or semi-distributed) models play an important role in interpreting and predicting the effects of LUCC on the hydrological processes of river basins. However, conventional distributed (or semi-distributed) models, such as the soil and water assessment tool (SWAT), generally assume that no LUCC takes place during the simulation period to simplify the computation process. When applying the SWAT, the subject river basin is subdivided into multiple hydrologic response units (HRUs) based on the land use/cover type, soil type, and surface slope. The land use/cover type is assumed to remain constant throughout the simulation period, which limits the ability to interpret and predict the effects of LUCC on hydrological processes in the subject river basin. To overcome this limitation, a modified SWAT (LU-SWAT) was developed that incorporates annual land use/cover data to simulate LUCC effects on hydrological processes under different climatic conditions. To validate this approach, this modified model and two other models (one model based on the 2000 land use map, called SWAT 1; one model based on the 2009 land use map, called SWAT 2) were applied to the middle reaches of the Heihe River in northwest China; this region is most affected by human activity. Study results indicated that from 1990 to 2009, farmland, forest, and urban areas all showed increasing trends, while grassland and bare land areas showed decreasing trends. Primary land use changes in the study area were from grassland to farmland and from bare land to forest. During this same period, surface runoff, groundwater runoff, and total water yield showed decreasing trends, while lateral flow and ET volume showed increasing trends under dry, wet, and normal conditions. Changes in the various hydrological parameters were most evident under dry and normal climatic conditions. Based on the existing research of the middle reaches of the Heihe River, and a comparison of the other two models from this study, the modified LU-SWAT developed in this study outperformed the conventional SWAT when predicting the effects of LUCC on the hydrological processes of river basins.