Disclosed is a disk drive that determines dynamic fly height (DFH) head non-linearity. A processor of the disk drive controls operations in the disk drive including: estimating a first and second set of head media spacing (HMS) actuation data for a DFH head at a first and second data frequency by commanding the application of power to the DFH head across a pre-defined power range; determining a first and second HMS value based upon the first and second sets of HMS actuation data; calculating a difference value between the first and second HMS values; determining whether the difference value exceeds a threshold.