Accurate quantification of sensible (H) and latent (LE) heat fluxes are desperately crucial for agricultural irrigation strategy, drought monitoring, water resource management, and climate change. Regional-scale H and LE were derived generally from satellite remote sensing data using relevant modeling methods. However, one of the challenges of modeling methods is to deal with sub-pixel heterogeneity, because the model usually assumes homogeneous conditions within a pixel. In this study, a hybrid model, which coupled deep neural network (DNN) and the remote sensing-based two-source energy balance (TSEB) model, was developed to estimate H and LE at multiple spatial resolutions to further quantify the influence of pixel size on the modeled fluxes. First, the DNN-based land surface temperature (LST) estimation model was developed and validated. LST at multiple spatial resolutions (i.e., 1, 5, 10, 30, 100, and 1000 m) were generated by the DNN method using multi-source satellite data including the GaoFen-2 (GF-2, a Chinese high-resolution optical remote-sensing satellite), Sentinel-2, and Landsat-8 images, respectively. Then, the hybrid DNN-TSEB model was used to estimate H and LE at multi-pixel sizes. Finally, modeled H and LE at 1 ∼ 1000 m were validated by eddy covariance (EC) and optical-microwave scintillometer (OMS) flux observation. Results revealed that the DNN-based LST model was a potential approach to generate LST at multiple pixel sizes. The hybrid DNN-TSEB model can produce more accurate H and LE when different land cover types were discriminated over heterogeneous farmland (e.g., the average bias for H and LE at a spatial resolution of 1 m were −9 and −6 W/m−2, respectively). Besides, the deviation of modeled fluxes from the observations increased as the spatial resolution became coarser, particularly the pixel size was greater than 30 m (average bias for H and LE were −34 and 30 W m−2, respectively). However, the magnitude of bias of fluxes estimates remained unchanged when the pixel sizes of satellite data were between 100 and 1000 m. The more important finding was that the hybrid model was a promising approach, which can obtain accurate estimates of H and LE at a high spatial resolution. In addition, the performance of the model based on GF-2 data was better than that based on Sentinel-2 and Landsat-8 data. The results suggest that pixel heterogeneity should be considered when estimating H and LE over heterogeneous landscapes with various surface types.
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