In order to improve the operation efficiency and Robust of the underwater manipulator, the problem that the persistent disturbances and singularities are researched and solved. Methods The robust design is proposed from both software and hardware aspects. On the hardware side, increasing the structural stiffness of the manipulator and the joint driving force enhances the ability to counteract persistent disturbances; on the software side, optimizing control software design, setting joint limits, offline path planning, and pre-path simulation, as well as real-time singularity detection and clear, can help avoid singularities. Conclusion The tests under major operating conditions show that the manipulator’s robust design measures are effective, significantly improving its operational efficiency and capability, and achieving the expected goals.