Caragana intermedia, which is widely planted with implementing of the ecological engineering for combating desertification in Northwest China, has caused the phenomenon of shrub encroachment in desert steppe. Studying the effects of planted shrub encroachment on ecosystem evapotranspiration (ET) in desert steppe can not only reveal the mechanism how human activities change the water cycle of ecosystem in semi-arid areas, but also guide local government to implement ecological restoration and construction. Based on the physiological and ecological parameters of vegetation and the hydrothermal conditions of the desert steppe in Yanchi county, Ningxia Hui Autonomous Region, the Biome Bio-Geochemical Cycles (Biome-BGC) model and the Breathing Earth System Simulator (BESS) model were combined to simulate the evapotranspiration changes and its components with the planted shrub encroachment occurring in the desert steppe ecosystem. The effects of the planted shrub encroachment on regional evapotranspiration was also been evaluated by the simulated data. The results showed that the planted shrub in grassland has changed the structure and characteristics of vegetation, and the annual maximum leaf area index (LAI) increased from 0.20 to 0.67, which changed the interannual and intra-annual characteristics of LAI in the desert steppe ecosystem. The annual average evapotranspiration of the ecosystem increased from 251.74 mm to 281.42 mm with the planted shrub encroachment occurred in the desert steppe of Yanchi county. Planted shrub encroaching significantly increased the ecosystem evapotranspiration in desert steppe during the growing season. The highest daily evapotranspiration was in August, the average daily evapotranspiration of desert steppe ecosystem increased from 1.27 mm/d to 1.56 mm/d in this month during the planted shrub encroaching. Planted shrub encroachment in desert steppe increased the transpiration of ecosystem by an average of 1.35 times and the evaporation by 1.06 times, which reduced the proportion of evaporation in evapotranspiration and increased the proportion of transpiration correspondingly, and therefore changed the structure of ecosystem evapotranspiration. It can be concluded that the evapotranspiration of the regional ecosystem has been increased with a large number of shrubs planted in desert steppe for preventing desertification and recovering ecosystem. And these activities also changed the composition of water consumption in desert steppe and thereby had a great impact on the flux of water in the ecosystem. The conclusions of this research bring insight for ecosystem management and vegetation reconstruction in desert steppe in the future.