Underwater 3D shape scanning technique becomes popular because ofseveral rising research topics, such as map making ofsubmarine topography for autonomous underwater vehicle (UAV), shape measurement of live fish, motion capture of swimming human, etc. Structured light systems (SLS) based active 3D scanning systems are widely used in the air and also promising to apply underwater environment. When SLS is used in the air, the stereo correspondences can be efficiently retrieved by epipolar constraint. However, in the underwater environment, the camera and projector are usually set in special housings and refraction occurs at the interfaces between water/glass and glass/air, resulting in invalid conditions for epipolar constraint which severely deteriorates the correspondence search process. In this paper, we propose an efficient technique to calibrate the underwater SLS systems as well as robust 3D shape acquisition technique. In order to avoid the calculation complexity, we approximate the system with central projection model. Although such an approximation produces an inevitable errors in the system, such errors are diminished by a combination of grid based SLS technique and a bundle adjustment algorithm. We tested our method with a real underwater SLS, consisting ofcustom-made laser pattern projector and underwater housings, showing the validity ofour method.