The invention discloses a method for preparing medicine-carrying hydroxyapatite/poly glycolide-co-lactide (PLGA)/chitosan demixing microspheres. The method comprises the following steps of: dissolving isoniazide in deionized water, adding hydroxyapatite powder, stirring in a dark place, and freeze-drying to obtain powder; mixing PLGA and the powder uniformly to obtain a hydroxyapatite/PLGA commixed solution containing the isoniazide; dissolving chitosan in an acetic acid aqueous solution to obtain a chitosan solution; mixing the chitosan solution and a polyvinyl alcohol aqueous solution to obtain a chitosan/polyvinyl alcohol solution; and pouring the hydroxyapatite/PLGA commixed solution containing the isoniazide into the chitosan/polyvinyl alcohol solution, stirring under vacuum, washingby using water, and freeze-drying to obtain the medicine-carrying hydroxyapatite/PLGA/chitosan demixing microspheres. The prepared medicine-carrying composite microspheres are regular in spherical shapes, uniform in particle size distribution, high in envelop rate of medicines, long in in-vitro medicine release time and small in burst release; and a preparation process is simple, raw materials are readily available, and industrialization is easy to realize.