Multi-material 3D fabrication at the nanoscale has been a long-sought goal in additive manufacturing, with great potential for the direct construction of functional micro/nanosystems rather than just arbitrary 3D structures. To achieve this goal, researchers have introduced several nanoscale 3D printing principles, explored various multi-material switching and combination strategies, and demonstrated their potential applications in 3D integrated circuits, optoelectronics, biological devices, micro/nanorobots, etc. Although some progress has been made, it is still at the primary stage, and a serious breakthrough is needed to directly construct functional micro/nano systems. In this perspective, the development, current status and prospects of multi-material 3D nanoprinting are presented. We envision that this 3D printing will unlock innovative solutions and make significant contributions to various technologies and industries in the near future.