The three dimensional (3D) perception of the low-light underwater environment has always been a major challenge which greatly limits the underwater operations. In this paper, an underwater active vision measurement system based on binocular structured light is designed to achieve high precision 3D reconstruction. Firstly, the fusion technology of binocular camera and laser addresses underwater optical attenuation and feature sparsity. Then, in order to avoid the huge inertia caused by the overall movement of the system, a laser scanner based on the mirror-galvanometer is used to accomplish static scanning of the scene. Subsequently, considering the influence of multiple media, underwater refraction models including monocular imaging model, binocular ranging model, and binocular polar curve constraint model are systematically proposed. What’s more, the conventional checkerboard-based passive visual calibration method is ineffective for low-light waters. Therefore, a simple calibration block is designed, and a new multi-objective laser-based calibration algorithm based on laser geometric constraints is proposed. Finally, the effectiveness of the system is verified by analyzing the 3D reconstruction results of underwater objects.