In the process of lunar exploration, and specifically when studying lunar surface structure and thickness, the established lunar regolith model is usually a uniform and ideal structural model, which is not well-suited to describe the real structure of the lunar regolith layer. The present study aims to explain the geological structural information contained in the channel 2 LPR (lunar penetrating radar) data. In this paper, the random medium theory and Apollo drilling core data are used to construct a modeling method based on discrete heterogeneous random media, and the simulation data are processed and collected by the electromagnetic numerical method FDTD (finite-difference time domain). When comparing the LPR data with the simulated data, the heterogeneous random medium model is more consistent with the actual distribution of the media in the lunar regolith layer. It is indicated that the interior structure of the lunar regolith layer at the landing site is not a pure lunar regolith medium but rather a regolith-rock mixture, with rocks of different sizes and shapes. Finally, several reasons are given to explain the formation of the geological structures of the lunar regolith layer at the Chang’E 3 landing site, as well as the possible geological stratification structure.