For the artificial ground freezing (AGF) projects in highly permeable formations, the effect of groundwater flow cannot be neglected. Based on the heat transfer and seepage theory in porous media with the finite element method, a fully coupled numerical model was established to simulate the changes of temperature field and groundwater flow field. Firstly, based on the classic analytical solution for the frozen temperature field, the model’s ability to solve phase change problems has been validated. In order to analyze the influences of different parameters on the closure time of the freezing wall, we performed the sensitivity analysis for three parameters of this numerical model. The analysis showed that, besides the head difference, the thermal conductivity of soil grain and pipe spacing are also the key factors that control the closure time of the frozen wall. Finally, a strengthening project of a metro tunnel with AGF method in South China was chosen as a field example. With the finite element software COMSOL Multiphysics® (Stockholm, Sweden), a three-dimensional (3D) numerical model was set up to simulate the change of frozen temperature field and groundwater flow field in the project area as well as the freezing process within 50 days. The simulation results show that the freezing wall appears in an asymmetrical shape with horizontal groundwater flow normal to the axial of the tunnel. Along the groundwater flow direction, freezing wall forms slowly and on the upstream side the thickness of the frozen wall is thinner than that on the downstream side. The actual pipe spacing has an important influence on the temperature field and closure time of the frozen wall. The larger the actual pipe spacing is, the slower the closing process will be. Besides this, the calculation for the average temperature of freezing body (not yet in the form of a wall) shows that the average temperature change of the freezing body coincides with that of the main frozen pipes with the same trend.