The exploitation and utilization of renewable energy, construction of sustainable energy system has gradually become the consensus of the international community, the research of microgrid technology with solar, wind and other renewable energy generation is becoming more and more deeply. According to the needs of the development of microgrid technology, in this paper a better functional architecture system of centralized control system for optimizing microgrids with new energy power generation system is proposed. First, according to the layered and distributed idea, a system of physical architecture which can run in the situations of both coordination control and self-control is designed, the system is mainly divided into physical components layer and the central station layer; and then the paper proposes the functional architecture system, it describes all the function modules and their interactions. Finally emphatically introduces the real-time security and stability control, energy optimization scheduling and other function modules which can improve the utilization ratio of renewable energy. The research of this system will play an important role in improving the absorption capacity of renewable energy; reducing fossil energy consumption and environment pollution.