A novel microscopic full field three-dimensional deformation measurement system is proposed and implemented, which is based on stereo microscope and digital image correlation method. In order to realize the calibration of stereo microscope, a new high precision distortion model is offered by reconstructing a B-spline surface. By acquiring images of the high precision planar calibration target designed independently and constructing the relationship between the target plane and the free distortion image planes, a form of space B-spline surface is established. Then, a high-efficiency image correlation method is realized by using a symmetric sub-pixel refinement strategy. The process for three-dimensional measurements using the proposed system is presented. Experimental results show that, the root-mean-sqsuare (RMS) error of the calibration results for stereo microscope system is 0.03 pixel, the displacement measurement accuracy is better than 0.2 μm, and the standard deviation of strain measurement error is no more than 100 με. At the same time, the experimental results indicate that the proposed system is accurately and can solve the problem of microscopic full field three-dimensional deformation measurement comprehensively.