3D micro/nanostructures have a wide range of applications in metamaterials, integrated circuits and optoelectronic coupling devices, etc. However, 3D nanofabrication has always been a difficult problem in materials science and nanoengineering fields due to the influence of surface tension or capillary action at nanoscale. Here, using nanoscale strong electric field (NSEF) of the electron beam as a driving force, the diffusion flux, migration direction, and aggregation process of material atoms or nanoclusters can be accurately controlled to realize the direct writing of 3D micro/nanostructures. By this method, several ZnO nanocharacters and a vertical ZnO nanowire with a diameter of 18 nm are direct written successfully, and a spatial contact with a characteristic size of 8 nm is created. The direct writing process of a bud‐like nanostructure is also demonstrated on a NiCo2O4 nanorod. Finally, the electron beam direct writing mechanism is analyzed based on the electric field forces and electric potential. This 3D nanofabrication method shows the advantages of flexibility, controllability, and high real‐time ability, which are of great significance to solve the problems of direct writing of 3D nanostructures, material molding control at nanoscale, and electrical interconnection in integrated circuits.