The numerical manifold method (NMM) is a calculation method based on Galerkin's variation and contains a dual covering system. Therefore, the NMM can easily deal with the construction of high-order manifold elements and is convenient for adaptive analysis. This study employed the NMM to simulate steady-state and transient heat conduction problems. The system equations were derived and a penalty function method was applied to deal with the boundary conditions. By simulating calculation examples for a one-dimensional bar, cuboid rock specimens, and thick-walled cylinders, the process of solving steady-state and transient heat-conduction problems and the influence law of the temperature pattern are demonstrated. Moreover, the convergence and effectiveness of the NMM in handling two-dimensional (2D) steady-state and 2D transient heat conduction problems was verified.