In a commercial fiber-based quantum key distribution system, the local and signal optical fields are transmitted through long distance fibers by using time division multiplexing and polarization multiplexing. The state of polarization of the optical field is inevitably disturbed by random birefringence of the standard single-mode fiber caused by external complex environments. This drift of the state of polarization significantly affects the balanced homodyne detection results and the secret key rate. Therefore, the key technology of the dynamic polarization control unit is crucial for the system in a large-scale commercial application. We theoretically analyze and prove that the polarization control unit only needs the combination of two degrees of freedom when considering the result of an arbitrary polarization extinction ratio at the receiver of the system. To overcome the influence of polarization variations, we propose a chaotic monkey algorithm based on Bayesian parameter estimation method and implement intelligence algorithm on field programmable gate array (FPGA) hardware under pulsed light with an integral-type detector for the dynamic polarization control unit. The simulation results show that the optimal combination is four degrees of freedom and the optimal prior distribution is an exponential distribution among various distributions in the dynamic polarization control unit. According to the simulation results, the experimental results show that the achieved polarization extinction ratio is over 30 dB and the average time of polarization control is 400 μs for a single random polarization scrambling. By combining the dynamic polarization control unit with the system, we demonstrate the continuous variable quantum key distribution (CV-QKD) under a continuous polarization scrambling scope of 0－2 krad/s and verify its effectiveness. In addition, the methods presented will improve the performance of the system and expand the range of applications even under strong external disturbance.