Hydroxyapatite (HAP) is a typical biomaterial, and has been widely used in the bone surgery and dental restoration. Owing to its large specific surface area and high absorbability, HAP has also been used in drug delivery and wastewater treatment. Due to its good electromagnetic property, easy recyclability, and distinct magneto thermoelectric effect, magnetic nanoparticles also gain more attention. To take both advantages, the combination of magnetic materials and HAP has become an important research direction in recent years. Although the preparation of hydroxyapatite composite materials in the past was reported, most of them only focused on the compositing materials and lacked the systematic summary on the synthesis methods. Based on the two ways of introducing magnetism into hydroxyapatite, doping and coating, the classical preparation methods, advantages and disadvantages of magnetic hydroxyapatite as well as the related applications were reviewed. The key problems of further research and future trends were discussed, in order to provide reference for the in-depth research and development of magnetic hydroxyapatite.