The invention provides a phase decoding method, a device thereof and a quantum key distribution system. The method comprises: splitting an input optical pulse of an incident arbitrary polarization state into two optical pulses for transmission on two optical paths respectively, and combining the two optical pulses after relative time delay to output the beam, wherein the optical pulses before beamsplitting or at least one of the two optical pulses obtained by beam splitting during beam splitting to beam combining is phase modulated according to a quantum key distribution protocol, and the twoorthogonally polarized states of the input light pulse are controlled to differ from each other by an integer multiple of 2pi in the phase difference between the two optical paths during beam splitting and beam combining. The invention can effectively solve the influence of the random change of the polarization state of the optical pulse on the system stability, and realize the stable phase decoding of the anti-environmental interference. In addition, the present invention may employ an unequal arm Mach number. In Zehnder interferometer, the optical pulse can be decoded only once through thephase modulator, which reduces the insertion loss of the receiver and improves the efficiency of the system.