Natural bone has a unique micro-/nano-structure, which is composed of organic nanomaterials (collagen fibers) and inorganic nanomaterials (hydroxyapatite). Thus, compared with traditional synthetic materials, natural bone has incomparable advantages in biological, functional and mechanical properties. In the research of tissue engineering and regenerative medicine, biomaterial scaffold with micro-/nano-structures simulating the characteristics of natural bone tissue are one of the research focuses. In recent years, researchers have found that micro-/nano-structured biomaterials can effectively regulate cell proliferation, differentiation and migration, and have a strong ability to promote cell osteogenic differentiation, so as to promote bone tissue regeneration in vivo. In this article, we focus on reviewing recent research progress of biomaterial design on simulating the hierarchical characteristics of natural bone, analyzing the complicated interaction between micro-/nano-structured biomaterials and cells, and summarizing their applications in bone tissue engineering to provide new ideas for the design of biomaterials.