Stick-slip motion is the most well-known phenomenon in nano-tribology. Maier et al. previously studied the dependency of slip time on contact geometry. In their work, they were able to identify the intermediate state during slip motion. However, detailed study of this intermediate state is difficult due to the fast dynamics. In a friction force microscopy experiment, various parameters, such as surface roughness, temperature, defects, and oxidation condition, affect the tribological behaviors. Hence, current experimental techniques only measure the average or maximum friction and describe the simple shape of stick-slip motion. Molecular dynamics simulation represents an effective solution for this issue. Dong et al. reviewed the molecular dynamics simulation approach with regard to the nano-tribology. The advantage of molecular dynamics simulation is that it can provide detailed information and direct visualization of the tribological phenomena on a time scale of a few nanoseconds. In this study, we investigate the detailed mechanism of stick-slip motion in nanoscale. Molecular dynamics simulation precisely mimics friction force microscopy experiments. In molecular dynamics simulations, a crystalline Si tip slides on a graphene surface, and the tip size is varied. The simulation results provide evidence of the intermediate state during slip motion and reveal the hierarchical structure of the stick-slip motion in nanoscale. Detailed relations among stick-slip motion, contact geometry, and energy state are also analyzed.