Thermal damage for material with the presence of a cone defect is studied. Firstly, a three-dimensional thermal damage model is established. Then, the distribution of electric field intensity and temperature of defective Si irradiated by laser pulse is calculated by the method of FDTD. At the same time, melting threshold of the Si material with defect is calculated and its variation rule with the height of the defect is analyzed. The results show that, the redistributed electric field is different in different depth of material. The maximum electric field intensity in the plane of each xOy is periodically changed over the height of material. The maximum electric field intensity in the first period near the surface is the crest value throughout the material. The value of melting threshold of material is the lowest when height of defect is 240 nm.