To free two hands of the underwater manipulator operator, the BCI (brain-computer interface) technology is applied to underwater operational tasks in this paper, where the manipulator follows instructions transformed from the brainwaves. As the current brainwave-based manipulator control methods can't satisfy requirements for the actual underwater tasks in terms of real-time performance and accuracy, a control strategy is proposed for controlling the underwater manipulator via event-related potentials (ERP) of brainwaves (evoked by visual stimuli). The operator can quickly complete a given task after optimizing the visual evoked ERP interface and combining the characteristics of the brainwaves control and the underwater manipulator operation. Eight subjects are invited to conduct experiments on a self-developed experimental platform. The average accuracy of identifying an operator's intention, the system information transfer rate and the average control time of completing the task are 91.5%, 27.7 bits/min and 90.1 s, respectively. Comparing with the similar systems, the system performance of the proposed control strategy is better, and the operational efficiency satisfies the practical operational requirements.