Due to the limitation of the measurement accuracy of classical radio signals, the time comparison accuracy can only reach ns level. In this paper, a time comparison scheme of Beidou system based on microwave-optical entangled signal is proposed, which effectively combines the long-distance transmission advantage of microwave signal with the single photon detection advantage of optical signal by electro-opto-mechanical converter, and the phase difference is solved by a phase conjugate processor ,so as to calculate the accurate time difference information. Through theoretical analysis and simulation, it is proved that even if the quantum signal is under the condition of low entanglement degree, the proposed scheme can improve the time comparison accuracy to the ps level.