The Water and Energy transfer Processes in Cold Regions (WEP-COR) model is an improved version of the Water and Energy transfer Processes in Large basins (WEP-L) model that integrates a multi-layer frozen soil model to simulate the hydrological processes in cold regions and the heat fluxes at different depths of frozen soil. The temperature, water content, freezing depth of the soil, and daily discharge were simulated and compared with observations. The simulated and observed data were used to analyze the runoff flow components. The results showed that the WEP-COR model can effectively simulate the distributions of the soil temperature and water content. The average root mean squared errors of the temperature, unfrozen water content, total water content, and freezing depth of the soil were 1.21 °C, 0.035 cm3/cm3, 0.034 cm3/cm3, and 17.6 cm, respectively. The mean Nash–Sutcliffe efficiency and relative error of the daily discharge were 0.64 and 6.58%, respectively. Compared with the WEP-L model, the WEP-COR model simulated the discharge with higher accuracy, especially during the soil thawing period. This improvement was mainly due to the addition of the frozen soil mechanism. The WEP-COR model can provide support for agricultural and water resources management in cold regions.