A system and method for dynamic frequency adjustment for interoperability of differential clock recovery, comprising: a frequency generator for receiving a frequency reference clock signal and generating a plurality of frequency signals, the plurality of frequency signals being output from the frequency generator and each having a different frequency; a flexible distributor for receiving the plurality of frequency signals from the frequency generator, and transmitting selected frequency signals; and a plurality of differential units, each for receiving the selected frequency signals, applying a differential signal to the selected frequency signals, adding time stamps to the selected frequency signals, and outputting respective time stamped differential selected frequency signals.