A medical image comparison method is firstly to obtain plural images of the same body at different time points. Then, obtain a first feature point group by detecting feature points in the first image captured at a first time point, and a second feature point group by identifying feature points in the second image captured at a second time point. An overlapping image information is generated by aligning the second image with the first image according to the first and second feature point groups. Then, window areas corresponding to a first matching image and a second matching image of the overlapping image information are extracted one by one by sliding a window mask, and an image difference ratio for each of the window areas is calculated. In addition, a medical image comparison system is also provided.
