Quantum key distribution (QKD) system must be robust enough in practical communication. The system performance is notably affected by phase drift. For the fiber-based phase-encoded quantum key distribution system, the Faraday-Michelson QKD scheme can auto-compensate the birefringence of fiber, but phase drift caused by environment variations is still a serious problem in practical operation. In this paper, the major schemes to compensate for the phase drift are analyzed in detail and an “five-phase”effective active phase compensation method is proposed. The comparison with other two major active phase compensation schemes also given. The result shows that this method uses less time to acquire the parameter of phase drift with the same precision and it can be used in phase-encoded QKD systems without introducing additional devices.