Constructing digital war-field electromagnetic environment needs to model and simulate the transmitting course of electric waves combining various environment factors. The Parabolic Equation (PE) described model is suitable for computing the waveguide propagation characteristics from an area in the horizon to that over the horizon, and there is Split-Step Fourier Transform (SSFT) algorithm to resolve the model. But it is an iterative method based on step length and is difficult to be realized in parallels, thus it is difficult to meet the requirement time wise and bring the obstacles to constructing war-field electromagnetic environment fastly. This paper puts forward a parallel computing method based on matrix transposing, and realizes parallel computing of the algorithm by constructing two-dimensional matrixes and distributing them to different process in line or in row. The method makes full use of the operating ability of calculation clusters, decreasing computing time. The result of computer simulating shows that parallel algorithm can have a speedup as four times large as that of sequential algorithm, thus verifies the effectiveness of the method.