A disk drive has a head fly-height actuator wherein the head-disk spacing is controlled as a function of both the track, and the sector or sectors within the track, where data is to be read or written. The fly-height actuator may be a thermal actuator comprising a heater located on the slider near the read/write head. The fly-height controller (FHC) for the thermal actuator stores band control signal (BCS) values representative of heater power (Hp) to be applied to the thermal actuator when reading or writing to a data track in the associated band of tracks. The FHC also either calculates from a programmed equation or recalls sector control signal (SCS) values representative of an Hp increment to be applied to the thermal actuator depending on the sector or sectors where data is to be written. The FHC sums the appropriate SCS value with the appropriate BCS value to achieve the desired Hp, resulting in the optimal fly-height not only for the selected band but also for the selected sector or sectors.