The synthesized hydroxyapatite (HAP) based materials have the similar chemical composition with the main inorganic components in human hard tissues. Therefore, HAP based biomaterials are considered to have good biocompatibility, degradability and biological activity, and have been widely used in biomedical fields. So far, various nanostructural HAP and their synthesis methods have been reported. However, the preparation of biomimetic HAP materials with ordered structure is still a big challenge in the related research fields. In hard tissues including enamel, cortical bone and cancellous bone, HAP nanocrystals are usually arranged in a controlled and ordered structure, according to the distribution of human body forces. Therefore, the biomimetic HAP with ordered structure may be prepared through biomimicking the natural ordered microstructure in hard tissue, which is expected to further enhance the mechanical and biological properties of traditional HAP-based biomaterials. In recent years, various methods have been reported to prepare ordered HAP materials in microscopic scales, including alumina template, organic solvent/small molecule regulation, calcium hydrogen phosphate based phase transformation, polymer/protein induced mineralization, frozen casting, etc. Recently, the author and his coworkers reported a solvothermal method for preparing HAP nanowires, and further developed a superficial small moleculesmediated self-assembly strategy to prepare ordered HAP nanowires structure in macroscopic with controllable size and direction. Compared with the traditional disordered HAP materials, the biomimetic HAP with ordered structure may have good mechanical and biological properties, which is of scientific significance in the design, preparation and biomedical application of new inorganic biomaterials. This review highlights the research progress of biomimetic HAP materials with ordered structure, including the new structures, synthesis methods and regulation mechanisms. Finally, the current challenges and prospects of biomimetic HAP materials with ordered structure are given and discussed.