A manufacturing method of a flip chip package structure is provided and has following steps: providing at least one silicon substrate having a connecting surface and at least one conductive base attached to the connecting surface; arranging a graphene copper layer covering the conductive base; laminating a photoresist layer on the connecting surface, etching the photoresist layer to form a cavity corresponding to the conductive base, and a portion of the graphene copper layer corresponding to the conductive base being exposed on a bottom of the cavity; electroplating a copper material on the graphene copper layer, and the copper material being accumulated in the cavity to form a copper pillar; removing the photoresist layer and the graphene copper layer covered by the photoresist layer.