We report here a nano-electronic–mechanical storage mechanism with graphene flakes (GFs) revealed by in situ transmission electron microscopy observations accompanied by nano-manipulation and probing of electrical properties. Repeatable two- and three- level state storage was demonstrated using two GFs nanoelectrodes with evident hysteresis properties. The detailed mechanisms, including the formation and rupture of the GFs contact as well as the corresponding electrical properties of the hysteresis, were visualized directly. Due to the high mechanical stability and outstanding electrical conductivity of the graphene, the hysteresis property is quite stable, which allows multi-value storage in this system. This work provides a route to achieve multiple value storage based on the nano-electronic–mechanical storage mechanism.