Provided is a core structure of an inductor element. The manufacturing method thereof is to embed a magnetic conductor including at least one magnetic conductive layer in a core body and to from a plurality of apertures for passing coils around the magnetic conductor in the core body. Accordingly, the magnetic conductor is designed in the core body by using the integrated circuit carrier board manufacturing process, such that the overall size and thickness of the inductor element can be greatly reduced, thereby facilitating product miniaturization using the inductor element.