In order to overcome the convolutional perfectly matched layer′s shortcoming of the poor absorption effect on evanescent wave in the finite difference time domain algorithm, a method of adding special absorption layer after convolutional perfectly matched layer was proposed. Without increasing the distance between the object and the inner layer of the absorbent layer, the decay factors in the special absorption layer were adjusted to make them constants and the absorption factor was increased from 1 to 10 to enhance the absorption layer′s absorption performance to the evanescent wave. An example in which the plane wave is incident vertically to the single-layer photonic crystal shows that the absorption boundary with the addition of the special absorption layer can keep the convergence of the calculation result when the distance from the scatterer is 5 mesh, while the traditional absorption boundary is required to be separated by 80 grids to ensure the results converge. By using this absorption boundary in the structure, the transmission characteristic curve of the multilayer photonic crystal was calculated and compared with the result obtained by the conventional method, the results were in good agreement with each other. The numerical results show that the method is effective and correct.