A system and method for calibrating and controlling a magnetic recording disk drive fly-height actuator uses the signal from the magnetoresistive (MR) read head to determine head-disk contact (HDC). The MR signal is measured over a low-frequency range, with the slider out-of-contact with the disk, to develop a reference value. The MR signal is then measured over the same low-frequency range and if it exceeds the reference value by some predetermined amount, this is an indication of HDC. The fly-height actuator control signal value for HDC is recorded and thus corresponds to a head-disk spacing of zero. The calibration method also determines the sensitivity of head-disk spacing to the fly-height actuator control signal by measuring a series of MR read signal amplitudes for a corresponding series of control signals. The fly-height actuator is calibrated from the sensitivity and the value of control signal that results in zero head-disk spacing, and can then be controlled to move the head to a desired fly height and maintain it at the desired fly height.