In seasonally frozen soils, liquid water and water vapor movement are critical in numerous environmental and engineering areas. However, the process of soil water movement becomes complicated due to the coexistence of liquid water, water vapor, and ice, and the underlying mechanisms are not yet fully understood. Based on the theory of coupled water, vapor, and heat transport, the modified HYDRUS-1D freezing module was used to investigate the mechanisms of soil water transfer in a cold region. Compared with its previous version, the newly developed model overcomes the numerical instability caused by the phase transformation between liquid water and ice. The verification results showed that the modified model was numerically stable and highly accurate, indicating its suitability for the study region. The variations in soil temperature, water content, water storage, evaporation, and drainage displayed typical seasonal patterns during the analyzed period, reflecting the effects of freeze–thaw cycles and rainfall-infiltration processes. Liquid flow, driven by a water potential gradient, played a major role under most environmental conditions, except when the soil was frozen when it became negligible. In comparison, vapor flow, driven by a temperature gradient, dominated soil water flow when ice was present and accounted for a considerable proportion of the total water flux in dry conditions, proving its significance for affecting soil water transport. These results clarified the mechanisms of soil liquid water and water vapor transfers in seasonally frozen soils and provided more insights for deepening the hydrological cycle theory.