With the rapid development of organizational immunology, numerous studies have demonstrated that the local immune microenvironment plays a central regulatory role in the repair and regeneration processes of various tissues, including skin, nerves, myocardium, and bones. The phenotype of innate immune cells is crucial for effective tissue repair, and immune regulation may serve as an effective approach to promote repair and enhance regenerative therapies. The rise of nanobiotechnology has opened up new methods for immunomodulation of nanomedicine and has brought hope for tissue regeneration and repair. Biomaterials can guide the immune response, which is essential for effective tissue regeneration, by modulating how immune cells respond to injury and how they facilitate repair processes. Thus, actively adjusting the host’s immune-inflammatory response by designing biomaterials to create a pro-regenerative immune microenvironment has become a groundbreaking approach in tissue engineering. This article discusses the roles of various subsets of immune cells in the repair and regeneration of bone, cartilage, and soft tissues, while also introducing the latest advancements in biomaterials that facilitate tissue repair. It subsequently focuses on the design and functional characteristics of immunomodulatory nanosystems and their applications in tissue repair. Finally, the article addresses the current challenges and future development prospects of immunomodulatory nanomaterials, aiming to provide improved outcomes for patients with acute and chronic wounds.