Taking the Loess Plateau of Northern Shaanxi Province as the research area, we quantitatively evaluated the water yield effects of the Grain for Green Program (GFGP) using InVEST water yield model, based on the principle of water balance and hydrological process. The simulation and calculation mainly considers the natural factors such as precipitation, evapotranspiration, soil, vegetation and land use/cover change factors in 2000 and 2010. The results show that the area of woodland, scrub and grassland increased by 122.7, 285.2 and 3, 204.0 km2 respectively in this decade, and farmland decreased by 3, 984.5 hm2 in total, which mainly converted to the land uses above. The implementation of GFGP had begun to show its effects. During this decade, the water yield of the research area displayed a decreasing tendency, with the total decrease of more than 890×106 m3 in Yan’an region and 720×106 m3 in Yulin region. Meanwhile, the spatial distribution of the decrease was highly consistent with the spatial extent of the GFGP. The land use/cover change had led to a total decrease of 116.654×106 m3 in water yield in the research area, among which the conversion from farmland to woodland, scrub and grassland contributed most to the decrease, which was 112.542×106 m3, accounting for 96.5% of the total decrease. The gradation based on the significance of water yield and spatial division adopted in this study can provide some technical support for the management of ecosystems and implementation of the GFGP in the Loess Plateau of Northern Shaanxi Province.