The variations of marine current speed may cause strong power fluctuations, which is extracted by Marine Current Turbine (MCT). In this paper, an Energy Management System (EMS) is presented for MCT system with Lithium-ion battery and Ultra-Capacitor (UC). According to the characteristics of each different energy unit, the system is used to smooth the power fluctuation and optimize power distribution. The model of marine current power is built firstly. Then, introduce the charging and discharging principle of bidirectional DC/DC converters, and design the current control method. Lastly, the EMS based on two first-order low pass filters is applied to determine the reference power of different unit. A simulation model of the system is built in MATLAB/SIMULINK and an experiment platform of hybrid Energy Storage System (ESS) is built for marine current power generation in lab. The results show that the proposed energy management strategy can be used to smooth power fluctuations, and optimize power distribution effectively.