One of the scientific payloads of Chang’E-5 (CE-5), i.e., the lunar penetrating array radar (LRPR), will carry out the in situ exploration of the regolith structure and guide the drilling sampling process. To evaluate the performance of the LRPR system, we present a multifrequency full-waveform inversion (FWI) with the total variation (TV) regularization constraint using simulated CE-5 LRPR data for imaging the regolith structure and estimating the physical parameters (permittivity and conductivity). The multifrequency FWI strategy is used to improve the inversion resolution, which updates the low-frequency gradient for the deep region and then increases the frequency range to update the shallow region. The TV regular-ization constraint not only reduces the gradient noise but also improves the inversion accuracy of local structures. To evaluate the actual LRPR measurement scenario, we use the actual source wavelet obtained from the LRPR instrument prototype in a ground lab to replace the theoretical Ricker wavelet. The actual source includes the effect of antenna radiation patterns and clutter noise from the metallic lander. Two typical heterogeneous lunar regolith model tests demonstrate that the proposed FWI scheme effectively reduces the lander metal impact, provides a reliable way to estimate the lunar regolith physical parameters and image the subsurface structures.