South Korea is currently in the preparatory stage of commercializing an ocean thermal energy conversion (OTEC) system, as the demonstration of a 1 MW scale OTEC system has been accomplished. However, the commercialization of OTEC requires the establishment of a control system for various environmental changes. Therefore, pre-emptive identification of the system’s risk factors and the process of analyzing the impact of the system, building control items, and optimizing control are necessary. This study aims to establish and analyze an optimized control system for MW-scale OTEC risk factors, such as the shutdown of seawater or refrigerant pumps. The selected OTEC system was designed for 1070 kW class facilities, with a 36.6% portion of total electricity usage by the seawater pump and refrigerant pump. As a result, an on/off control system was adopted in order to eliminate the risk factors. By adjusting this option, dry operation of the refrigerant pump, water hammering, and liquid inflow into the turbine were successfully prevented. To be more specific, the initial system was to be shut down due to a sharp decrease in power at the point where the deep seawater flow rate was 538 kg/s (35.7% of max flow rate) and the surface seawater flow rate was 715 kg/s (38.4% of max flow rate). This situation was improved by adopting parallel operation of seawater pumps and on/off control, thereby leading to a more stabilized operation by maintaining a flow rate of over 1864 kg/s for surface seawater and 1507 kg/s for deep seawater. Moreover, it was confirmed that the flow rate of the pump was reduced by 1.89 kg/s per second in the process of pump shutdown during a single operation mode of the refrigerant pump. Parallel operation made it possible to maintain 60.2% of the output by increasing the power of the second pump’s flow rate in the event of the first pump shutting down. The final seawater temperature differential power generation model derived from this study consists of two refrigerant pumps and two surface seawater and deep seawater pumps in order to prevent system shutdown caused by a single pump failure. The final design was reflected in the final delivery to Kiribati, which is located near the equator.