Abstract: In the numerical simulation of ground penetrating radar (GPR), to attenuate the evanescent wave generated by the thickness of the truncated area or the influence of parameters, a new method is proposed to use the complex frequency shifted perfectly matched layer (CFS-PML) as the absorption boundary and combined with the higher-order finite element method (HO-FEM) in the frequency domain to solve the distribution of the total electromagnetic field components. The method improves the properties of the dielectric intrinsic tensor matrix in the truncated domain and uses the matrix frequency shift parameter α to absorb the evanescent wave and improve the absorption performance at the grazing angle. Numerical experiments are conducted on the method. Compared with the traditional PML, the accuracy of the HO-FEM method combined with CFS-PML is significantly improved, the reflection error is reduced by 10−30 dB extra, and the calculation time is saved by 17%−30%. In addition, the method can be applied to the calculation of the total electromagnetic field of a complex geological structure model, which provides a new method for the numerical simulation of geological lidars.