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This paper studies the smart control issue for an autonomous microgrid in order to maintain the secure voltages as well as maximize economic and environmental benefits. A control scheme called as multi-agent based hierarchical hybrid control is proposed versus the hierarchical control requirements and hybrid dynamic behaviors of the microgrid. The control scheme is composed of an upper level energy management agent, several middle level coordinated control agents and many lower level unit control agents. The goals of smart control are achieved by designed control strategies. The simulations are given to demonstrate the effectiveness of proposed smart control for an autonomous microgrid.