Microscopic vision systems based on a stereo light microscope (SLM) are used in microscopic measuring fields. Conventional measuring methods output the disparity surface based on stereo matching methods; however, these methods require that stereo images contain sufficient distinguishing features. Moreover, matching results typically contain many mismatched points. This paper presents a novel method for disparity surface reconstruction by combining an SLM and laser measuring techniques. The surfaces of small objects are scanned by a laser fringe, and a stereo image sequence containing laser stripes is obtained. The central contours of the laser stripes are extracted, and central contours are derived for alignment. A disparity coordinate system is then defined and used to analyze the relationship between the motion direction and reference plane. Next, the method of aligning disparity contours is proposed. The results show that our method can achieve a precision of ±0.5 pixels and that the real and measured shapes described by the disparity surface are consistent based on our method. Our method is confirmed to perform much better than the conventional block-matching method. The disparity surface output obtained by our method can be used to measure the surface profiles of microscopic objects accurately.