The travel time and amplitude of ground-penetrating radar (GPR) waves are closely related to medium parameters such as water content, porosity, and dielectric permittivity. However, conventional estimation methods, which are mostly based on wave velocity, are not suitable for real complex media because of limited resolution. Impedance inversion uses the reflection coefficient of radar waves to directly calculate GPR impedance and other parameters of subsurface media. We construct a 3D multiscale stochastic medium model and use the mixed Gaussian and exponential autocorrelation function to describe the distribution of parameters in real subsurface media. We introduce an elliptical Gaussian function to describe local random anomalies. The tapering function is also introduced to reduce calculation errors caused by the numerical simulation of discrete grids. We derive the impedance inversion workflow and test the calculation precision in complex media. Finally, we use impedance inversion to process GPR field data in a polluted site in Mongolia. The inversion results were constrained using borehole data and validated by resistivity data.