One aluminum sample whose surface was treated with anode oxidation and one fiber reinforced plastics sample were used in this study, one side of both samples were milled six flat-bottom wedges with different depth. Pulsed thermography was used to obtain the temperature decay data series, the temperature-time curves of different positions in each wedge were extracted to approximately simulate that the same depth defects were affected with different levels of three-dimensional heat diffusion, and the extracted data can also approximately represent the temperature decay of defects with different ratio of defect size over defect depth (RDSD). The theoretical procedures of thickness measurement were analyzed based on one-dimensional heat conduction model, and the corresponding results were analyzed to compare how the defect size influences the defect depth measurement under the same thickness. The results indicate that the characteristic times of different methods approximately linearly increase with RDSD, and its slope is bigger when defect is deeper or thermal diffusivity is smaller.