A compact binocular stereo vision system was used for measurement in small scale. This paper analyzed the influence of CCD pixel discontinuity on the measurement accuracy and then built the relationship between structural parameters (baseline,focal length and object distance) and distance measurement errors. When considering the discontinuity of pixels,the relationship curve about measuring distance and disparity was of a stair-step shape. The measurement error decreased with the increase of the baseline and the focal length,while it gradually increased along with the object distance. The measurement accuracy of our system can reach 98.89%. Our valuable theory can be offered for optimization design of the binocular stereo vision system which is applied in small scale measurement.