A preparation method of polyvinyl alcohol/hydroxyapatite (PVA/HA) composite microspheres belongs to preparation methods of composite water-in-oil emulsion system microspheres. PVA and HA precursors are used as raw materials to prepare a clear and transparent mixed solution; the clear and transparent mixed solution is dispersed into an oil phase containing a surfactant to form a homogeneous water-in-oil microemulsion; and the PVA/HA composite microspheres can be finally obtained by successive crosslinking reaction under acid-catalyzed conditions, HA deposition under alkaline conditions, product centrifugation, washing, drying and other processes. The method has the advantages of simple process, good repeatability, low energy consumption and low cost, and effectively solves the problems that inorganic nanoparticles are easy to agglomerate in the microspheres to cause uneven structures and poor comprehensive performances and the like. The composite microspheres prepared by the method have the advantages of regular morphology, high dispersibility, uniform microstructure, good biocompatibility, biological activity and adsorption performance, and can be used as drug carrier materials, bone repair materials, environmental water treatment materials, cosmetics or food additives and the like.