A disk drive is disclosed comprising a plurality of disk surfaces, and a head actuated over each disk surface, where each head comprises a fly height actuator (FHA) operable to control a fly height of the head over the corresponding disk surface. A fly height is measured for each head to generate a plurality of fly height measurements. An average value is generated in response to the plurality of fly height measurements, and a first control value is generated for a first head based on the average value and the fly height measurement for the first head. The first FHA of the first head is controlled in response to the first control value.