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Small crater morphology method has been used extensively in lunar regolith thickness estimation. However, topographic degradation can change crater morphology and thus bias regolith thickness estimation. In this study, we first developed a shape model for small fresh craters with normal, central mound, flat-bottomed, and concentric geometry. We then simulated their degradation processes by using a topographic diffusion model. Simulation results show that as a small crater degrades, its morphology changes from concentric/central mound to flat-bottomed, from flat-bottomed to normal, and from normal to invisible, depending on its initial morphology. Upon the time a crater becomes invisible, its diameter can be enlarged by a factor of ∼70%. We proposed a revised small crater morphology method and applied it to the Apollo 11 and 14 landing sites. Our revised method permits a more accurate estimate of regolith thickness, and our results are helpful in understanding the evolution of the Moon’s surface.