［Purposes ］ This paper aims to clarify the seepage heat transfer process and the stress deformation characteristics of the lining structure in highly geothermal tunnels，so as to provide a theoretical basis for safe tunnel construction.［Methods］ This paper proposed to use the local thermal non -equilibrium （LTNE） model to study the seepage heat transfer process in highly geothermal tunnels and improved the thermo -hydro -mechanical （THM） full coupling calculation method in COMSOL Multiphysics software by customizing the partial differential equations （PDEs）.The accuracy of the method was verified，and the THM coupling responses of Nige highly geothermal tunnel were studied using this method.［Findings］ There is a large temperature difference between the surrounding rock and groundwater in the Nige highly geothermal tunnel，and the groundwater seepage is the main reason for this difference.The lining structure of the tunnel not only effectively supports the surrounding rock but also blocks the free discharge of groundwater into the tunnel because of its low permeability，resulting in the accumulation of heat in the surrounding rock behind the lining and the increase in the temperature difference between the inner and outer sides of the lining structure.Under the joint action of seepage heat transfer and THM coupling effect，the deformation of the lining structure of the Nige tunnel changes from the vertical compression deformation under normal temperature to the horizontal compression deformation，and the high -stress zone of the vault and the bottom of the tunnel appears a large range of plastic deformation.［Conclusions ］ The LTNE model can more truly reflect the seepage heat transfer process of highly geothermal tunnels and better explain the mechanism of temperature difference between surrounding rock and groundwater in highly geothermal tunnels.The THM coupling analysis method using the LTNE model is more suitable for the safety evaluation of a highly geothermal tunnel structure with groundwater seepage.