Water and energy processes in frozen soils are important for better understanding hydrologic processes and water resources management in cold regions. To investigate the water and energy balance in seasonally frozen soils, CoupModel combined with the generalized likelihood uncertainty estimation (GLUE) method was used. Simulation work on water and heat processes in frozen soil in northern China during the 2012/2013 winter was conducted. Ensemble simulations through the Monte Carlo sampling method were generated for uncertainty analysis. Behavioral simulations were selected based on combinations of multiple model performance index criteria with respect to simulated soil water and temperature at four depths (5 cm, 15 cm, 25 cm, and 35 cm). Posterior distributions for parameters related to soil hydraulic, radiation processes, and heat transport indicated that uncertainties in both input and model structures could influence model performance in modeling water and heat processes in seasonally frozen soils. Seasonal courses in water and energy partitioning were obvious during the winter. Within the day-cycle, soil evaporation/condensation and energy distributions were well captured and clarified as an important phenomenon in the dynamics of the energy balance system. The combination of the CoupModel simulations with the uncertainty-based calibration method provides a way of understanding the seasonal courses of hydrology and energy processes in cold regions with limited data. Additional measurements may be used to further reduce the uncertainty of regulating factors during the different stages of freezing–thawing.