The invention of silica based bioactive glass in the late 1960s sparked a strong interest in exploring various silicon containing biomaterials from macroscopic to nanoscale. In the past few decades, considering the outstanding biological activity, excellent biocompatibility, ease of surface functionalization, and controllable synthesis of these biomaterials, extensive exploration has been conducted on their potential in various biomedical applications. However, in order to accelerate clinical translation and unexpected utilization of silicon in nanomedicine and biomaterial composition, it is highly necessary to comprehensively understand its characteristics and biological effects from a holistic perspective. In this review, we comprehensively discuss the latest developments in silicon-based biomaterials, including their classification, characteristics, manufacturing methods, and multifunctional biomedical applications. In addition, we also focused on the multidimensional design of pure silicon and mixed silicon nanomedicines and biomaterials, as well as their inherent biological effects and interactions with biological systems. Their extensive biomedical applications cover from drug delivery and bioimaging to therapeutic interventions and regenerative medicine, demonstrating the importance of their rational design and manufacturing in meeting specific requirements and optimizing their therapeutic diagnostic performance. In addition, we also provide insights into the future prospects and potential challenges of silicon nanomedicine and biomaterials. By revealing these exciting research advances, we aspire to promote further progress in the biomedical field and drive the development of innovative silicon nanomedicine and biomaterials, with revolutionary applications in the biomedical field