The invention presents a single lens auto focus system of stereo image generation and a method thereof. The stereo three-dimensional (3D) image capturing method of a single lens auto focus camera, includes the steps of a) taking plural multi-focus images; b) estimating the plural multi-focus images to obtain a depth map and an all-in-focus image; c) mixing the depth map with plural background depth maps to obtain a mixed depth map; d) obtaining respectively a left image for left eye of user and a right image for right eye of user by means of depth image based rendering (DIBR); and e) outputting the left image and the right image, thereby displaying a stereo image onto a 3D display.