As a calculation method based on the Galerkin variation, the numerical manifold method (NMM) adopts a double covering system, which can easily deal with discontinuous deformation problems and has a high calculation accuracy. Aiming at the thermo-mechanical (TM) coupling problem of fractured rock masses, this study uses the NMM to simulate the processes of crack initiation and propagation in a rock mass under the influence of temperature field, deduces related system equations, and proposes a penalty function method to deal with boundary conditions. Numerical examples are employed to confirm the effectiveness and high accuracy of this method. By the thermal stress analysis of a thick-walled cylinder (TWC), the simulation of cracking in the TWC under heating and cooling conditions, and the simulation of thermal cracking of the Swedish Äspö Pillar Stability Experiment (APSE) rock column, the thermal stress, and TM coupling are obtained. The numerical simulation results are in good agreement with the test data and other numerical results, thus verifying the effectiveness of the NMM in dealing with thermal stress and crack propagation problems of fractured rock masses.