Heterogeneous nanowires having a core-shell structure consisting of single-crystal apatite as the core and graphitic layers as the shell and a synthesis method thereof are provided. More specifically, provided is a method capable of producing large amounts of heterogeneous nanowires, composed of graphitic shells and apatite cores, in a reproducible manner, by preparing a substrate including an element corresponding to X of X5(YO4)3Z is a chemical formula for apatite, adding to the substrate a gaseous source containing an element corresponding to Y of the chemical formula, adding thereto a gaseous carbon source, and allowing these reactants to react under optimized synthesis conditions using chemical vapor deposition (CVD), and to a method capable of freely controlling the structure and size of the heterogeneous nanowires and also to heterogeneous nanowires synthesized thereby.