The Source Region of the Yellow River (SRYR), renowned as the “Water Tower of the Yellow River”, serves as an important water conservation domain in the upper reaches of the Yellow River, significantly influencing water resources within the basin. Based on the Weather Research and Forecasting (WRF) Model Hydrological modeling system (WRF-Hydro), the key variables of the atmosphere–land–hydrology coupling processes over the SRYR during the 2013 rainy season are analyzed. The investigation involves a comparative analysis between the coupled WRF-Hydro and the standalone WRF simulations, focusing on the hydrological response to the atmosphere. The results reveal the WRF-Hydro model’s proficiency in depicting streamflow variations over the SRYR, yielding Nash Efficiency Coefficient (NSE) values of 0.44 and 0.61 during the calibration and validation periods, respectively. Compared to the standalone WRF simulations, the coupled WRF-Hydro model demonstrates enhanced performance in soil heat flux simulations, reducing the Root Mean Square Error (RMSE) of surface soil temperature by 0.96 K and of soil moisture by 0.01 m3/m3. Furthermore, the coupled model adeptly captures the streamflow variation characteristics with an NSE of 0.33. This underscores the significant potential of the coupled WRF-Hydro model for describing atmosphere–land–hydrology coupling processes in regions characterized by cold climates and intricate topography.