With graphene as a well-known representative, two-dimensional (2D) atomic crystals are single-layer or few-layer crystalline materials. It is significant to investigate the structure evolution of the 2D atomic crystals in electronic movement process, because it relates to the stability of material properties and the feasibility of the device application. Here, the pinhole evolution of few-layer graphene during electron tunneling and electron transport was observed using in situ transmission electron microscopy (TEM). For few-layer graphene with defects, pinholes expanded with an increase on the electron tunneling current and time, respectively. However, during electron transport processes, with increasing current and time, both, expansion and shrinkage behaviors could be observed among the pinholes distributed within the graphene nanosheet. These behaviors are the result of competition between sublimation and self-repair. Both types of pinhole evolution aim to form a smooth surface with lower surface free energy. The critical boundary conditions for the sublimation and self-repair are determined by the temperature, graphene pinhole structure and active graphene fragment. These findings provide significant reference for the stability of graphene structure and the reliability of graphene based electronic device.