In microgrids, the distributed generators (DG) can be used as distributed compensators so as to compensate the voltage unbalances in the critical bus. However, the power quality disturbance in generator sides and local buses may be affected and exceeds the limit. It can be more convenient to implement tertiary control so as to adjust the compensation efforts among DGs and ensure the acceptable power quality in local buses. Moreover, as centralized control methods have certain disadvantages, such as low flexibility, expandability and heavy computation burden, this paper proposes an agent-based distributed hierarchical control method. Communication links are required between neighboring units. Consensus algorithm and optimization algorithm are implemented in tertiary control for global information discovery and local optimal decision-making respectively. The tertiary control gives lower level controller a tertiary compensation gain to adjust the local DG compensation effort so as to ensure the acceptable power quality in the local bus while keeping the best power quality in critical bus. Simulation results are shown to demonstrate the effectiveness of the method.