Evapotranspiration (ET) is an important part of surface–atmosphere interactions, connecting the transfer of matter and energy. Land surface heterogeneity is a natural attribute of the Earth’s surface and is an inevitable problem in calculating ET with coarse resolution remote sensing data, which results in significant error in the ET estimation. This study aims to explore the effect and applicability of the evaporative fraction and area fraction (EFAF) method for correcting 1 km coarse resolution ET. In this study we use the input parameter upscaling (IPUS) algorithm to estimate energy fluxes and the EFAF method to correct ET estimates. Five ground stations in the midstream and downstream regions of the Heihe River Basin (HRB) were used to validate the latent heat flux (LE) calculated by the IPUS algorithm and EFAF method. The evaluation results show that the performance of the EFAF method is superior to that of the IPUS algorithm, with the coefficient of determination (R2) increasing, the root mean square error (RMSE) decreasing, and the mean bias error (MBE) decreasing by 17 W/m2 on average. In general, the EFAF method is suitable for correcting the deviation in LE estimated based on Sentinel data caused by land surface heterogeneity and can be applied to obtain accurate estimates of ET.