Cholesterol plays a significant role in the organization of lipids and modulation of membrane dynamics in mammalian cells. However, the effect of cholesterol depletion on the eukaryotic cell membranes seems controversial. In this study, the effects of cholesterol on the topography and mechanical behaviors of CHO-K1 cells with manipulated membrane cholesterol contents were investigated by atomic force microscopy (AFM) technique. Here, we found that the depletion of cholesterol in cell membranes could increase the membrane stiffness, reduce the cell height as well as promote cell retraction and detachment from the surface, whereas the cholesterol restoration could reverse the effect of cholesterol depletion on the membrane stiffness. Increased methyl-β-cyclodextrin levels and incubation time could significantly increase Young’s modulus and degree of stiffing on cell membrane and cytoskeleton. This research demonstratede importance of cholesterol in regulating the dynamics of cytoskeleton-mediated processes. AFM technique offers excellent advantages in the dynamic monitoring of the change in membranes mechanical properties and behaviors during the imaging process. This promising technology can be utilized in studying the membrane properties and elucidating the underlying mechanism of distinct cells in the near-native environment.