To improve the acquisition speed of polarized fluorescence images, a fluorescence microscopy system with high speed polarization is proposed based on the polarization direction control of exciting light with an electro optical modulator, and polarized fluorescence images are recorded with a camera. The polarization distortion induced by the excitation optical path is measured and precisely compensated to ensure the precision of polarization direction control on sample plane. The experimental system is tested with giant unilamellar vesicles. The results show that the proposed system can effectively map the orientation information of biomolecular at a video frame rate and can be used to monitor orientation information of dynamic sample molecules.