Following the general trend in the miniaturization of electronic devices, techniques that enable 3D printing at the nanometer scale are gaining momentum. As a widely used planar processing method, electron-beam lithography (EBL) can be employed to create 3D nanostructures in a layer-by-layer fashion. However, compared with other 3D printing techniques, EBL is limited by the stringent requirement of a range of fabrication equipment and complex fabrication processes. Here, we have demonstrated that EBL can be developed to a controllable 3D nanoprinting technology with the aid of ice resists. With carefully selected accelerating voltage, electron dose, and ice thickness, 3D objects can be efficiently printed in a single vacuum system through an iterative process of ice deposition and e-beam exposure. Mixed ice resists containing solid anisole and water are also introduced into the printing process, which offer a flexible control of the thickness of printed layers. Apart from carbonaceous objects obtained with our method, 3D printing of metals is also promising by employing organometallic compounds as ice resists. This study provides a fresh perspective in EBL-based nanofabrication and expands the spectrum of modern additive manufacturing.