In this paper, we studied a vibration problem that is critical and common to most precision measurement systems. For micro mechanical part measurements, results obtained from the vision-based precision measurement system may contain errors due to the vibration. In order to defeat this generic problem, for the current study, a PC based image processing technique was used first, to assess the effect of the vibration to the precision measurement and second, to develop an in-situ calibration algorithm that automatically compensate the measurement results in real time. We used a set of stereoscopic CCD cameras to acquire the images for the dimensional measurement and the reference measurement. The mapping function was obtained through the in-situ calibration to compensate the measurement results and the statistical analysis for the actual results is provided in the paper. Based on the current statistical study, it is expected to obtain high precision results for the micro measurement systems.