A method of controlling a flying height of a magnetic head of a hard disk drive apparatus includes producing a reference FOD (flying on demand) voltage profile defining a relationship between the flying height of the magnetic head and an FOD voltage at a measured temperature, wherein an end of the magnetic head thermally expands and protrudes when the FOD voltage is applied to a heater included in the magnetic head and setting the reference FOD voltage profile that is corrected using a reference maximum flying height of the magnetic head that is preset at room temperature, as an applied FOD voltage profile to control the flying height of the magnetic head.