In the receiving end of quantum key distribution (QKD) system based on the polarization encoded BB84 protocol, the polarization control system is very key to QKD. In order to recover and stabilize very efficiently the damaged polarization states owing to these factors including the optical fiber, environment temperature and so on, the performance of the electric polarization controller (EPC) is analyzed and rotation matrix is introduced as the Müeller matrix of the EPC. A strategy of avoiding the blind zone is put forward and the real-time polarization control algorithm is designed in the non-ideal situation. The algorithm shows that every control process uses only two degrees of freedom to transform all possible polarization states and can improve greatly the rate of the controlling. Simulation results show that this algorithm is feasible.