The exchange of moisture and energy between the land and the atmosphere plays a crucial role in terrestrial hydrological cycle and climate change. However, existing studies on the retrieval of surface water and heat flux tend to overlook the dynamic changes in surface vegetation and atmospheric aerosols, which directly affect surface energy and indirectly alter various meteorological factors, including cloud, precipitation, and temperature. In this study, we assess the machine-learning retrieval method for surface fluxes that takes into account vegetation changes and aerosol effects, using FLUXNET observations and remote sensing data to retrieve latent heat flux (LE) and sensible heat flux (H). We constructed four sets of deep neural network models: (a) The first set considers only meteorological factors, (b) the second set considers meteorological factors and aerosols, (c) the third set considers meteorological factors and vegetation changes, and (d) the fourth set comprehensively considers meteorological factors, aerosols, and vegetation changes. All model performances were evaluated using statistical indicators. ERA5 reanalysis and remote sensing data were used to drive the models and retrieve daily H and LE. The retrieved results were validated against ground observation sites that were not involved in model training or the FLUXCOM product. The results show that the model that considers meteorological factors, aerosols, and vegetation changes has the smallest errors and highest correlation for retrieving H and LE (RH = 0.85, RMSEH = 24.88; RLE = 0.88, RMSELE = 22.25). The ability of the four models varies under different vegetation types. In terms of seasons, the models that consider meteorological factors and vegetation changes, as well as those that comprehensively consider meteorological factors, aerosols, and vegetation changes, perform well in retrieving the surface fluxes. As for spatial distribution, when atmospheric aerosols are present in the region, the model that considers both meteorological factors and aerosols retrieves higher values of H compared to the model that considers only meteorological factors, while the LE values are relatively lower. The model that considers meteorological factors and vegetation changes, as well as the model that comprehensively considers meteorological factors, aerosols, and vegetation changes, retrieves lower values in most regions. Through the validation of independent observation sites and FLUXCOM products, we found that the model, considering meteorological factors, aerosols, and vegetation changes, was generally more accurate in the retrieval of surface fluxes. This study contributes to improving the retrieval and future prediction accuracy of surface fluxes in a changing environment.