Light changes its direction of propagation before entering a camera enclosed in a waterproof housing owing to refraction, which means that perspective imaging models in the air cannot be directly used underwater. In this article, we propose an accurate binocular stereo measurement system in an underwater environment. First, based on the physical underwater imaging model without approximation and Tsai’s calibration method, the proposed system is calibrated to acquire the extrinsic parameters, as the internal parameters can be pre-calibrated in air. Then, based on the calibrated camera parameters, an image correction method is proposed to convert the underwater images to air images. Thus, the epipolar constraint can be used to search the matching point directly. The experimental results show that the proposed method in this article can effectively eliminate the effect of refraction in the binocular vision and the measurement accuracy can be compared with the measurement result in air.