Magnetic core structure and manufacturing method thereof

A magnetic core structure and a manufacturing method thereof are provided. The magnetic core structure includes a magnetic core, a plurality of conductive layers, and two wires. The magnetic core has a winding column, and a first side column and a second side column that are connected to both ends of the winding column. The winding column includes two outer protrusions each having an accommodating groove. The first side column has two first setting stations, and the second side column has two second setting stations. The conductive layers are disposed on the two first setting stations and the two second setting stations. The two wires are wound on the winding column, and a part of the two wires are respectively located in the two accommodating grooves. In one of the two first setting stations and one of the two second setting stations that are located on one of both sides, one of the two wires is electrically coupled to one of the conductive layers on the first setting station and one of the conductive layers