Accurate estimation of shortwave radiation in mountains will advance our knowledge of climate change effects, especially on mountain ecosystems. Recently, some approaches have been developed to estimate shortwave radiation parameters in mountains with satellite data, but few attempts were made to understand the impacts of digital elevation model (DEM) uncertainty on estimates. Our study investigates such impacts quantitatively in clear-sky conditions at multiple spatial and temporal scales (30–3000 m, instantaneous to daily). We employed a retrieval algorithm to estimate instantaneous and daily mean clear-sky downward shortwave radiation (DSR) and net shortwave radiation (NSR), as a proxy for our evaluation. The accuracy of our method based on accurate terrain data was verified against in-situ measurements with root-mean-square errors (RMSEs) of 65.9 W/m2 and 65.1 W/m2 for instantaneous DSR and NSR, and 21.2 W/m2 and 22.5 W/m2 for daily mean values, respectively. When using satellite DEM products, the DSR estimation uncertainty could increase by 64.0% for instantaneous values and 46.2% for daily mean values. Using AW3D30 and SRTM DEMs for DSR estimation led to a maximum difference of 16.8% (103.6 W/m2) and 13.0% (25.8W/m2) on instantaneous and daily mean values, respectively. That estimation difference of shortwave radiation decreased with an increase in spatial scale, with RMS deviation lower than 2% for spatial resolution beyond 3000 m. In addition, the evaluation of introducing random errors into AW3D30 DEM showed that the shortwave radiation uncertainty caused by DEM may exceed the algorithm uncertainty itself with DEM mean absolute error (MAE) equaling about 5.0 m. Considering the current DEM accuracy, the impacts of DEM errors on shortwave radiation in mountains cannot be ignored. This study emphasizes the potential impacts of DEM uncertainty on surface shortwave radiation estimation, which is crucial in using satellite-derived datasets for energy balance calculation and climate change applications in mountains.