The present disclosure includes a configuration of a polarization control system and an algorithm that realize fast polarization controlling and tracking while avoiding the Glitch problems (i.e., loss of polarization tracking). The polarization controller includes multiple stages along with tunable orientation and retardation angles. The retardation angles are initialized to at least two different values for better polarization tracking in normal mode. In a normal mode, only the orientation angles of the polarization controller are dithered. When the monitored error is higher than the threshold, the polarization controller enters a glitch mode, and Glitch detection can be improved through error signal data processing. In the Glitch mode, at least one retardation angle is dithered along with the orientation angles. After the Glitch problem is avoided, the polarization controller stops dither the retardation angles and move all wave plates back to their initial values, and the polarization controller enters the normal mode.