In order to solve the problem of image distortion of the three-dimensional reconstruction underwater, a model based on the non-parallel binocular stereo vision system was proposed, which could transfer the image shooted through a plat waterproof cover underwater into the image shoted in air, and general conditions were presented to use it. When the focus of lens is on the surface of the water, there is a one-to-one correspondence between the underwater image and the image-without-water. If the focus of lens is outside the water, the proposed model still valid when the distance from the focus to the object is far greater than the focal length and the distance from the focus of lens to refractive surface along z axis. Three-dimensional reconstruction of the feature points was used in experiments to verify the validity of the model. The results show that with the mentioned method, the average coordinate errors of the feature points are 2.23%(x), 1.51%(y), 1.10%(z), respectively, compared with the actual one. The proposed model provides a basis of applying the three-dimensional image reconstruction.