The freeze-thaw process influences moisture and heat transport, which is of great importance for the runoff and groundwater infiltration processes. At present, the research on the freeze-thaw process is mainly conducted by means of field/laboratory experiments. The mechanism and details of the fluid and heat flow characteristics are still poorly understood. In this study, we developed the code to realize the elaborate description of each thermo-hydraulic phenomenon during the entire freeze-thaw process. Based on the framework of TOUGH2, we improved the EOS3 module to realize the function of phase transition between water and ice. The improved model can handle the system of water/air two components in gas/liquid/solid three phases. Moreover, the absolute and relative permeability change and thermal conductivity correction induced by the occurrence of the ice phase are all considered. The long-term field monitoring was conducted on two sites to observe the entire freeze-thaw process in the Changbai Mountain area. The monitoring data were used to verify the code and get a satisfactory result. It is found that the freeze-thaw process could be briefly divided into three stages, the gradually freezing stage, long-term stable stage, and a prompt thaw stage. The proposed method provides a solution for the in-depth investigation of the moisture and heat migration, and groundwater dynamics in seasonally frozen areas.