This paper introduces the evaluation results of nondestructive detection of the wall paintings in the Yuan Dynasty tombs in Pucheng, Shaanxi Province using the square-heating thermograph. For this purpose, a three-dimensional thermal tomography quantitative evaluation method for reconstructing the heat storage coefficient of the material is proposed, and the results are compared with the post-processing results of pulse phase thermal imaging and principal component thermal imaging. The experimental results show that the three methods can improve the defect detection ability, but the three-dimensional thermal tomography method can realize the quantitative three-dimensional assessment of the internal disease distribution of the mural. Finally, three-dimensional thermal tomography is performed on one of the entire murals. The proposed method can realize the detection and evaluation of hollow drums, cracks, and wall support structures, and can provide useful evaluation methods and reference information for mural removal, restoration and protection, and mural research.