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