Evapotranspiration (ET) plays an import role in transferring water and converting energy in the land‒atmosphere system. Accurately estimating ET is crucial for understanding global climate change, ecological environmental problems, the water cycle, and hydrological processes. Machine learning (ML) algorithms have been considered as a promising method for estimating ET in recent years. However, due to the limitations associated with the spatial–temporal resolution of the flux tower data commonly used as the target set in ML algorithms, the ability of ML to discover the inherent laws within the data is reduced. In this study, a hybrid framework was established to simulate ET in data-deficient areas. ET simulation results of a coupled model comprising the Budyko function and complementary principle (BC2021) were used as the target set of the random forest model, instead of using the flux station observation data. By combining meteorological and hydrological data, the monthly ET of the Inner Mongolia section of the Yellow River Basin (IMSYRB) was simulated from 1982 to 2020, and good results were obtained (R2 = 0.94, MAE = 3.82 mm/mon, RMSE = 5.07 mm/mon). Furthermore, the temporal and spatial variations in ET and the influencing factors were analysed. In the past 40 years, annual ET in the IMSYRB ranged between 241.38 mm and 326.37 mm, showing a fluctuating growth trend (slope = 0.80 mm/yr), and the summer ET accounted for the highest proportion in the year. Spatially, ET in the IMSYRB showed a regular distribution of high ET in the eastern region and low ET in the western area. The high ET value areas gradually expanded from east to west over time, and the area increased continuously, with the largest increase observed in the 1980s. Temperature, precipitation, and normalized difference vegetation index (NDVI) were found to be the most important factors affecting ET in the region and play a positive role in promoting ET changes. These results provide an excellent example of long-term and large-scale accurate ET simulations in an area with sparse flux stations.