Embodiments of the present invention provide a magnetic disk drive capable of suppressing variations in flying height of a magnetic head caused by decrease in the amount of a low density gas inside a housing and a control method therefore. According to one embodiment, the magnetic disk drive includes a magnetic head, a magnetic disk, and a housing containing the magnetic head and the magnetic disk, wherein the housing is filled with a low density gas having a lower density than air. An amount of the low density gas in the housing is estimated and, based on the amount of the low density gas, a flying height of the magnetic head from a surface of the magnetic disk is controlled.