With the development of marine economy, the demand for underwater observation and prospecting equipment is increasing accordingly. Conventional underwater vision system can only provide image but lack of 3D information. To realize 3D measurement for various underwater applications, a binocular stereo vision system is investigated in this paper. Different with classical stereo vision problem, the challenge for underwater stereo vision system mainly comes from the light reflection between camera lens and water. Based on the proposed underwater stereo vision model and calibration method, a prototype of underwater 3D vision system is established. The system contains two cameras and the light-based illumination module, which can work under the water depth of 30 m. The experiments are implemented in the pool and near sea environments. Experimental results show that, the system has an observing distance up to 8 m in normal water condition. The effective measurement range is 0.5-4.5 m, and the measurement error varies from 2 to 20 mm with the increasing of observing distance. Precision of the proposed system can meet most underwater measurement requirement, and has great potentials in underwater observing and engineering applications.