The physical effects such as random birefringence of fiber optic channels due to environmental influences make the optical signals transmitted in them have sensitive polarization variations, which seriously affects the performance of polarization biased code quantum key distribution systems. In this paper, a low-noise fiber channel wavelength division multiplexing real-time polarization compensation system is presented, where single photon counting is used as a feedback signal. The system can acquire the fiber channel polarization change information by detecting the photon counting of the conjugate reference light. In the system, the compensation algorithm is designed to control the electric polarization controller to calibrate the polarization state of the quantum signal light under the corresponding polarization base in real time, and the stable fiber channel polarization compensation is successfully achieved. In order to verify the effectiveness of the compensation system, a quantum key distribution test based on BB84 protocol with a transmission distance of 25.2 km is conducted, and stable test results of up to 8 hours are obtained in the laboratory environment and the simulated metropolitan area network buried fiber environment, with the average quantum bit error rate being 0.52% and 1.25%, respectively. The experimental results show that this system can guarantee the stable operation of polarization-encoded quantum key distribution in the buried fiber environment in urban areas.