Bone defect repair is a complex process of bone regeneration. Bone substitute implanted at the bone defect sites act as three-dimensional scaffolds that guide and promote bone regeneration. The function of orthopedic implants is often limited by complicating factors such as insufficient integration into host tissue, inflammatory reactions, and infection. Biological behaviors of immune cells and osteogenesis-related cells on these bone biomaterials are largely determined by the surface properties. The advances in nanofabrication technology have help us fabricated a range of nanostructured surface with controlled physicochemical properties to modulate the behaviors of osteogenesis-related cells and immune cells, thus affecting bone integration and local immune reaction. In this review, we summary the development of nanostructured surface modification to bone implants with controlled physicochemical properties, including roughness, wettability, surface charge and topography. In particular, we focus on the effect of nanotopographies on cell recruitment and cellular adhesion, osteogenic differentiation, mineralization and osseointegration, antibacterial activities, and modulation of immune response.