In this paper, we combine the modified equivalent current approximate method and graphical electromagnetic computing method to solve the electromagnetic scattering problems in the missile target covered with the thermal protective layer. The modified equivalent current approximate method is used to calculate the lossy dielectric and combining graphical electromagnetic method, and using a computer display technology, blanking and occlusion, a three-dimensional surface is projected on a computer screen, and the pixels are calculated. The calculation in three-dimensional space is converted into the calculation in two-dimensional space, thereby greatly reducing the computation time and complexity. The results show that when the incident frequency is low, the thickness of the thermal protection layer does not affect the radar cross section value. When the frequency is increased with the thickness of the thermal protection layer, the radar cross section value continuously decreases, which indicates that the thermal barrier coating is a lossy medium: the bigger the imaginary part of the dielectric, the stronger the ability to consume the energy is and the more obvious the change of missile radar cross section is. When the thermal protective layer has pores, the higher the porosity, the greater the value of the radar cross section is; when the porosity is zero, the value of the radar cross section is minimal; when the porosity is the same, the thinner the thermal protection layer, the bigger the radar cross section is. When the projectile phenomenon occurs, it does not affect the radar cross section.