This paper examines the radar penetration into a rough soil surface with a vertical moisture profile. Numerical analysis shows that the penetration depth occurs at a larger dynamic range of incident angle in V polarization but in H polarization. The maximum polarization difference occurs at low frequencies (e.g., L band) and at a large incident angle (e.g.,70°~85°), which are rarely used due to low backscattering returns. Of the two roughness parameters, the RMS height significantly influences on the penetration depth more than the correlation length. The dependence of penetration depth on the wave polarization moderates when the surface becomes rougher. Results also suggest that the penetration depth is sensitive to the inhomogeneity of moisture profiles due to the temporal evaporation process, indicating that the penetration depth is difficult to quantitate and an equivalent model to estimate it may be inappropriate, or at least it is difficult to establish.