Atomic force microscopy (AFM) enables us to evaluate the physical properties of the surface of materials on a nanoscale. Using a coarse-grained molecular dynamics (CG-MD) simulation, this study investigated the molecular deformation mechanisms of polycarbonate (PC) during AFM nano-indentation experiments. By using the coarse-grained (CG) force field of PC, the nano-indentation deformation behavior of PC was simulated. During this process, the AFM tip is used to penetrate the polymer surface and then withdrawn completely; the PC then undergoes local elastoplastic deformation. To investigate the deformation mechanism at a molecular scale, we quantitatively evaluated the variations in the potential energy associated with different molecular deformation modes, such as bond stretching, bending, and torsion. It was found that the bending mode of the molecular chain plays a critical role in the onset of yielding. Furthermore, the spatial variations of the potential energy were investigated. They indicate that the variation of the potential energy of the bending mode is significant when undergoing nano-indentation. The CG-MD simulation results were then compared with the experimental results. They indicate that our computation accurately reproduces the experimental indentation force-displacement curves. Therefore, the present CG-MD simulation can successfully model experimental AFM nano-indentation. This may be useful for the discussion of the molecular deformation mechanisms of PC and related polymer materials.