High-speed is one development tendency of the practical and commercial quantum key distribution (QKD) systems, and the gain-switched semiconductor laser (GSSL) and Sagnac interferometer have been popular components for high-speed commercial polarization-based BB84 QKD systems thanks to their stability, compactness and low cost. However, due to the finite extinction ratio (ER) of the GSSL, the time-dependent source side-channel, which is theoretically presented in [Phys. Rev. A106(6): 062618 (2022)10.1103/PhysRevA.106.062618], also exists in these QKD systems. In this article, we experimentally investigate this side-channel in the polarization-based BB84 QKD system. The results show an obvious correlation in the output polarization states between the weak leakage light and its adjacent pulses, which will cause information to leak. More importantly, we have proposed several countermeasures, retested the side channel, and developed a mathematical framework to quantitatively assess the impact of the time-dependent side channel and these countermeasures on the secure key rate. Finally, we offer a trade-off analysis that considers defense effectiveness, pulse impact, and cost for various countermeasures in QKD. This provides a practical recommendation for improving the security of QKD systems.