With the development of biotechnology, biomaterials have been rapidly developed and shown great potential in bone regeneration therapy and bone tissue engineering. Nanoparticles have attracted the attention of researches and have applied in various fields especially in the biomedical field as the special physicochemical properties. Nanoparticles were found to regulate bone remodeling depending on their size, shape, composition, and charge. Therefore, in-depth research was necessary to provide the basic support to select the most suitable nanoparticles for bone relate diseases treatment. This article reviews the current development of nanoparticles in bone tissue engineering, focusing on drug delivery, gene delivery, and cell labeling. In addition, the research progress on the interaction of nanoparticles with bone cells, focusing on osteoblasts, osteoclasts, and bone marrow mesenchymal stem cells, and the underlying mechanism were also reviewed. Finally, the current challenges and future research directions are discussed. Thus, detailed study of nanoparticles may reveal new therapeutic strategies to improve the effectiveness of bone regeneration therapy or other bone diseases.