Geothermal resources are composed of rock and water, in which water-rock interaction (WRI) has a great influence on the physical properties of thermal reservoirs. The Red River Fault is abundant in different kinds of geothermal resources and the main thermal reservoirs are sandstones and limestones. The study has used the water chemistry, X-ray diffraction (XRD), N2 adsorption, mercury injection, scanning electron microscopy (SEM), physical parameters, and WRI simulation experiments to study the physical properties changes in thermal reservoirs. The pores of thermal reservoirs are mainly intragranular and intergranular pores, in which sandstones are dominated by micropores and mesopores while limestones are dominated by macropores. Through the WRI simulation experiment, the reservoirs have generated many dissolution pores and microfractures, of which the pore-throat connectivity has deteriorated. The changes of physical parameters can be divided into two stages with opposite trends, in which the first stage is controlled by temperature and pressure while the second stage is influenced by dissolution and precipitation. The study has suggested that the change stage of physical properties should be clarified to update the resource quantity dynamically in the development process and the components of fracturing fluids should be studied to achieve the optimal improvement of physical properties and reduce the adverse impact on pore-throat connectivity before the development engineering.