A write head's material having a great thermal expansion coefficient expands due to Joule heat resulting from a write current and a temperature rise dependent on high-frequency core loss, thereby causing the head's flying surface to protrude toward a magnetic disk. This phenomenon is called TPR (thermal protrusion). It is essential that the flying height be accurately determined and managed in consideration of TPR. A magnetic disk drive for actual use or a magnetic disk drive that is in a testing process but similar to the one for actual use is used to measure TPR amount changes resulting from a write operation, store the resulting measured data in a memory or on the magnetic disk, and perform flying height management with the stored measured data. Further, flying height management is performed as needed in conjunction with a SMART function. The present invention makes it possible to perform high-reliability flying height management.