A magnetic component structure with thermal conductive filler, including two magnetic cores combining together to form an inner accommodating space and at least one core opening, two plate portions connect each other through an inner leg structure and two outer leg structures, a bobbin sleeving on the inner leg structure, a coil winding on the bobbin, a bobbin housing surrounding the bobbin and the coil winding and form winding opening facing the at least one core opening, gaps are formed between the encasing structure constituted by the bobbin housing and the bobbin sleeving and the magnetic cores, a thermal conductive filler formed between the bobbin and the bobbin housing and encapsulating at least parts of the coil winding, and a cooling surface contacts the magnetic cores and the thermal conductive filler, the thermal conductive filler extends outwardly to contact the cooling surface through the opening and the winding opening.