The invention relates to a binary hybrid energy storage device in a distributed power generation system and the distributed power generation system. The binary hybrid energy storage device in the distributed power generation system comprises a first bidirectional DC/DC converter, a second bidirectional DC/DC converter, a second Boost circuit, a super-capacitor bank, a storage battery pack and a control device. The first bidirectional DC/DC converter is connected with the super-capacitor bank. The second bidirectional DC/DC converter is connected with the storage battery pack. The super-capacitor bank and the storage battery pack are connected via the second Boost circuit. The control device controls is connected with the first bidirectional DC/DC converter, the second bidirectional DC/DC converter and the second Boost circuit in a control way. When the distributed power supplies are insufficient in generating capacity and cannot meet the load demand, power outputted by the power generation system can be fully utilized by the device to buffer fluctuation energy of the distributed power supplies under the circumstances so that storage batteries can be protected.