Probes of nano scale are a type of important tools for the study on nano-film material. Dynamic explicit method accompanied by the intermittent feeding of probe to dissipate the energy is applied to avoid the difficulty of convergence in the finite element model for a system of probe, graphene, and substrate. And the results of a static state are obtained from this strategy. The functions of interface interaction forces are deduced from adhesion energy and the potential between atoms. The force functions are implanted into subroutines in Abaqus code to simulate the interactions among graphene layers, probe, and substrate. Results of simulations show good consistency with the data of experiments.