In a commercial fiber-based quantum key distribution (QKD) system, the state of polarization (SOP) of the optical fields is inevitably disturbed by random birefringence of the standard single-mode fiber due to an external complex environment. We analyze theoretically the effect of SOP fluctuations on the continuous-variable (CV) QKD system and experimentally verify its validity. To overcome the influence of the polarization variations, a self-adaptive gradient algorithm is proposed to achieve high-speed polarization controlling under pulsed light with field programmable gate array hardware. For single random polarization scrambling, the polarization extinction ratio achieved is over 30 dB and the average time of polarization control is 827 $\ensuremath{\mu}\mathrm{s}$. In order to eliminate further the effect of the occasional failures of polarization control, we properly filter the raw keys in terms of the relative phase fluctuations between the signal and the local oscillator. By combining this approach with the high-speed polarization control, we demonstrate a CV QKD under a continuous polarization scrambling of 314 rad/s. Our results provide useful references for practical application of fiber-based CV QKD in a field environment.
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