A rapid autofocus method for a stereo microscope includes steps of: calculating a disparity of each of stereo microscopic images in a stereo microscopic calibration image sequence; extracting a clear stereo microscopic image sequence from the stereo microscopic calibration image sequence; then, finding out a largest disparity and a smallest disparity among the disparities of all the stereo microscopic images in the clear stereo microscopic image sequence; at a chosen magnification, arbitrarily acquiring a stereo microscopic image; finally, determining a disparity range according to the disparity of the acquired stereo microscopic image, the largest disparity and the smallest disparity, and realizing an autofocus of a target object in the acquired stereo microscopic images. The disparity range is obtained via once off-line calibration at the same magnification, and applicable to the autofocus at an arbitrary timing.