Based on the evaluation principle of the measuring uncertainty of the traditional coordinate measuring machine (CMM), the analysis and evaluation of the measuring uncertainty for optical micro-CMM have been made. Optical micro-CMM is an integrated measuring system with optical, mechanical, and electronic components, which may influence the measuring uncertainty of the optical micro-CMM. If the influence of laser speckle is taken into account, its longitudinal measuring uncertainty is 2.0 μm, otherwise it is 0.88 μm. It is proved that the estimation of the synthetic uncertainty for optical micro-CMM is correct and reliable by measuring the standard reference materials and simulating the influence of the diameter of laser beam. With Heisenberg's uncertainty principle and quantum mechanics theory, a method for improving the measuring accuracy of optical micro-CMM through adding a diaphragm in the receiving terminal of the light path was proposed, and the measuring results are verified by experiments.