A method for eliminating flicker of a multi-exposure imaging system is provided. The method includes the steps of: capturing a long exposure image based on a long exposure from a scene; capturing a short exposure image based on a short exposure from the scene; obtaining an exposure ratio of the long exposure to the short exposure; generating a long accumulated value by accumulating pixel values of a portion of the long exposure image; generating a short accumulated value by accumulating pixel values of a portion of the short exposure image corresponding to the portion of the long exposure image; and generating a flicker gain according to the long average value, the short average value and the exposure ratio.