A head flying height control method includes the steps of: detecting contact of a head having a heater with a corresponding storage medium, and associating the amount of heat generated by the heater when the contact is detected with a situation where the flying height of the head is zero; measuring at least one type of characteristics that are the saturation characteristics of the read margin of data written on the storage medium with the head, and the saturation characteristics of the electromagnetic conversion characteristics of the head, the measuring step being carried out every time the flying height of the head is varied, with a reference being the situation where the flying height of the head is zero, the current used for writing the data being a parameter in the saturation characteristics; and adjusting the flying height of the head, based on the measurement result of the measuring step.