This paper examines the radar penetration into a rough soil surface with a vertical moisture profile. Numerical analysis shows that the penetration depth decreases exponentially with increasing frequency, and the difference between H- and V- polarization reduces. For the incident angle dependence, the variation of penetration depth is somehow complex. For incident angle larger than 20^o, the penetration depth decreases at H polarization, but increases first and then decreases at V polarization. As for soil surface dependence, the topsoil moisture content has a greater impact on the penetration depth than the surface roughness. Of the two roughness parameters, the rms height has a more significant influence on the penetration depth than the correlation length. The dependence of penetration depth on the wave polarization moderates when the surface becomes rougher. Results 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 measure and an equivalent model to estimate it may be inappropriate, or at least it is difficult to establish.