As a new generation of materials/structures, heterostructure is characterized by heterogeneous zones with dramatically different mechanical, physical or chemical properties. This endows heterostructure with unique interfaces, robust architectures, and synergistic effects, making it a promising option as advanced biomaterials for the highly variable anatomy and complex functionalities of individual patients. However, the main challenges of developing heterostructure lie in the control of crystal/phase evolution and the distribution/fraction of components and structures. In recent years, additive manufacturing techniques have attracted increasing attention in developing heterostructure due to the unique flexibility in tailored structures and synthetic multimaterials. This review focuses on the additive manufacturing of heterostructure for biomedical applications. The structural features and functional mechanisms of heterostructure are summarized. The typical material systems of heterostructure, mainly including metals, polymers, ceramics, and their composites, are presented. And the resulting synergistic effects on multiple properties are also systematically discussed in terms of mechanical, biocompatible, biodegradable, antibacterial, biosensitive and magnetostrictive properties. Next, this work outlines the research progress of additive manufacturing employed in developing heterostructure from the aspects of advantages, processes, properties, and applications. This review also highlights the prospective utilization of heterostructure in biomedical fields, with particular attention to bioscaffolds, vasculatures, biosensors and biodetections. Finally, future research directions and breakthroughs of heterostructure are prospected with focus on their more prospective applications in infection prevention and drug delivery.