Numerical simulation of three-layer layered electromagnetic waves is key problem for nondestructive testing of ground penetrating radar (GPR) pavement. In this paper, the difference iterative scheme of three-dimensional first-order symplectic partitioned Rung-Kutta is derived, which is applied to pavement detection of ground penetrating radar by using Higdon ABC boundary condition. Incident waves are considered as line sources. The accuracy and efficiency of the proposed algorithm are verified by the traditional 3D-FDTD algorithm. The results indicate that the accuracy and efficiency between the two methods are consistent. Unlike the traditional 3D-FDTD algorithm, the CPU time of the proposed method is reduced by 30%. The diseases location of the pavement structure is directly reflected by the numerical simulation result of the proposed method. This provides a three-dimensional symplectic partitioned Rung-Kutta algorithm, which can be applied to the forward simulation of GPR. It provides a three-dimensional symplectic partitioned Rung-Kutta algorithm, which can be applied to the forward simulation of GPR. The accurate electromagnetic response information of the target can be obtained by the proposed method.