To better solve the problem of target detection in marine environment and to deal with the difficulty of 3D reconstruction of underwater target, a binocular vision-based underwater target detection and 3D reconstruction system is proposed in this paper. Two optical sensors are used as the vision of the system. Firstly, denoising and color restoration are performed on the image sequence acquired by the vision of the system and the underwater target is segmented and extracted according to the image saliency using the super-pixel segmentation method. Secondly, aiming to reduce mismatch, we improve the semi-global stereo matching method by strictly constraining the matching in the valid target area and then optimizing the basic disparity map within each super-pixel area using the least squares fitting interpolation method. Finally, based on the optimized disparity map, triangulation principle is used to calculate the three-dimensional data of the target and the 3D structure and color information of the target can be given by MeshLab. The experimental results show that for a specific size underwater target, the system can achieve higher measurement accuracy and better 3D reconstruction effect within a suitable distance.