Abstract: For the wave scattering problem of 3D regional sites under plane wave incidences, the free field considering non-uniform distributed nodes of the spectral element method (SEM) is derived by using analytical method, which is used as the input wave filed for wave motion simulations based on the SEM. The motions of interior nodes are computed using the high-order SEM, and the motions of the boundary surface nodes are obtained by applying the multi-transmitting formula (MTF). In addition, a parallel computation across nodes is realized by using the message passing interface (MPI) technique. Then, the parallel simulations of 3D wave scattering problems base on SEM are achieved. Finally, the accuracy and stability performance of the proposed method are validated by some typical numerical examples. The results show that the presented method can achieve high simulation accuracy for the 3D local site scattering problem under plane wave incidence in different polarization directions. Up to the third order MTF, under the condition that the stability of the internal domain computation is ensured, a long-time stable calculation results can be obtained when the artificial wave velocity of the MTF is taken to be close to the shear wave velocity of the corresponding boundary nodes, and no other additional treatments are needed to eliminate the high-frequency oscillations. The low-frequency drift instability of the MTF can be easily eliminated by applying quite small modification parameters, and the simulation accuracy is generally unaffected by it. The method of this paper has promising application prospect in the numerical simulations of regional 3D ground motion under plane wave incidences.