Refraction-induced errors affect the accuracy of three-dimensional visual measurements in deepwater environments. In this study, a binocular camera refractive imaging model was established, and a calibration method for the refraction parameters was proposed for high-accuracy shape and deformation measurements in deep-water environments. First, an initial estimate of the refractive axis was obtained using a three-dimensional calibration target. Then, the errors in the distance between the spatial point pairs and the reprojection errors are taken as the dual optimization objectives, and the Non-dominated Sorting Genetic Algorithm II is applied to optimize the refraction parameters. To efficiently calculate the reprojection error, an improved numerical computation method is proposed to accelerate the calculation of the analytical forward projection. Underwater experiments were conducted to verify the method's effectiveness. The results showed that the average error of the absolute position of the reconstructed points was less than 1.1 mm and the average error of the displacement was less than 0.04 mm. This study provides a sound solution for accurate three-dimensional visual measurement in deep-water environments.