Underwater manipulators are important robotic tools in the exploration of the ocean environment. Up to now, most existing underwater manipulators are rigid and with fixed 5 or 7 degrees of freedom (DOF), which may not be very suitable for some complicated underwater scenarios (e.g., pipe networks, narrow deep cavities, etc.). The biomimetic concept of muscles and tendons is also considered as continuum manipulators, but load capacity and operation accuracy are their essential drawbacks and thus limit their practical applications. Recently, the cable-driven technique has been developed for manipulators, which can include numerous joints and hyper-redundant DOF to execute tasks with dexterity and adaptability and thus they have strong potential for these complex underwater applications. In this paper, the design of a novel cable-driven hyper-redundant manipulator (CDHRM) is introduced, which is driven by multiple cables passing through the tubular structure from the base to the end-effector, and the joint numbers can be extended and decided by the specific underwater task requirements. The kinematic analysis of the proposed CDHRM is given which includes two parts: the cable-joint kinematics and the joint-end kinematics. The geometric relationship between the cable length and the joint angles are derived via the established geometric model for the cable-joint kinematics, and the projection relationship between the joint angles and end-effector’s pose is established via the spatial coordinate transformation matrix for the joint-end kinematics. Thus, the complex mapping relationships among the cables, joints and end-effectors are clearly achieved. To implement precise control, the kinematic control scheme is developed for the CDHRM with series-parallel connections and hyper-redundancy to achieve good tracking performance. The experiment on a real CDHRM system with five joints is carried out and the results verify the accuracy of kinematics solution, and the effectiveness of the proposed control design. Particularly, three experiments are tested in the underwater environment, which verifies its good tracking performance, load carrying and grasping capacity.