Master-slave system is a vital technique for controlling robot motions. An intuitive master controller enables precise and easy control of robot, especially for underwater robotics applications. Most of the commercially available master-slave systems are very complex and expensive, and operators need to receive extensive training before being able to correctly operate the robot. This paper addresses these problems by introducing a simple and intuitive master controller for an experimental semi-autonomous underwater vehicle equipped with 3-link dual-arm. The master controller includes a vehicle main master controller and two units of 3-link manipulator master controller. Moreover, each end-tip of the manipulator master controller is attached with a vehicle sub-master controller that consists of a joystick and tactile switches. These sub-master controllers are designed to control the position and attitude of the vehicle. The ability to simultaneously control two units of 3-link dual-arm and the position and attitude of the vehicle is the uniqueness of the proposed controller. In this work, the design of the developed master controller and the structure of a unilateral master-slave system are presented. The usefulness of the master controller is verified through experiment on controlling an actual dual-arm underwater robot to catch a target object in underwater environment.