The PLL phase stabilization principle was theoretically analyzed to solve the problem of phase differencestability between multi-channel singular frequency signals. Further, a multi-channel singular-frequency phasedifference stabilization algorithm was proposed to solve the greatest common divisor between frequencies and simultaneouslyoutput frequencies to meet the requirements of phase difference stability.The testing results indicate thatphase difference stabilities are less than 4° when the output frequencies are in the S-band,satisfying the requirementswhile effectively verifying the feasibility and flexibility of the algorithm.