Estimating daily continuous evapotranspiration (ET) can significantly enhance the monitoring of crop stress and drought on regional scales, as well as benefit the design of agricultural drought early warning systems. However, there is a need to verify the models’ performance in estimating the spatiotemporal continuity of long-term daily evapotranspiration (ETd) on regional scales due to uncertainties in satellite measurements. In this study, a thermal-based two-surface energy balance (TSEB) model was used concurrently with Terra/Aqua MODIS data and the ERA5 atmospheric reanalysis dataset to calculate the surface energy balance of the soil–canopy–atmosphere continuum and estimate ET at a 1 km spatial resolution from 2000 to 2022. The performance of the model was evaluated using 11 eddy covariance flux towers in various land cover types (i.e., savannas, woody savannas, croplands, evergreen broadleaf forests, and open shrublands), correcting for the energy balance closure (EBC). The Bowen ratio (BR) and residual (RES) methods were used for enforcing the EBC in the EC observations. The modeled ET was evaluated against unclosed ET and closed ET (ETBR and ETRES) under clear-sky and all-sky observations as well as gap-filled data. The results showed that the modeled ET presented a better agreement with closed ET compared to unclosed ET in both Terra and Aqua datasets. Additionally, although the model overestimated ETd across all different land cover types, it successfully captured the spatiotemporal variability in ET. After the gap-filling, the total number of days compared with flux measurements increased substantially, from 13,761 to 19,265 for Terra and from 13,329 to 19,265 for Aqua. The overall mean results including clear-sky and all-sky observations as well as gap-filled data with the Aqua dataset showed the lowest errors with ETRES, by a mean bias error (MBE) of 0.96 mm.day−1, an average mean root square (RMSE) of 1.47 mm.day−1, and a correlation (r) value of 0.51. The equivalent figures for Terra were about 1.06 mm.day−1, 1.60 mm.day−1, and 0.52. Additionally, the result from the gap-filling model indicated small changes compared with the all-sky observations, which demonstrated that the modeling framework remained robust, even with the expanded days. Hence, the presented modeling framework can serve as a pathway for estimating daily remote sensing-based ET on regional scales. Furthermore, in terms of temporal trends, the intra-annual and inter-annual variability in ET can be used as indicators for monitoring crop stress and drought.