This article presents an enhanced hierarchical control framework of microgrids, as an effective complementary of conventional hierarchical control, to improve operation efficiency and perform thermal management. The enhanced hierarchical control framework is implemented by two control levels. In primary control level, droop control strategy with active thermal management is proposed to perform identical thermal sharing among paralleled inverters. Furthermore, secondary control level is developed to improve operation efficiency and perform thermal management in system-level according to time-varying load profiles, where finite state machine model is adopted to optimize operation number of inverters. In addition, in grid-connected microgrid, resonance phenomena may be caused by time-varying grid impedance. Hence, resonance mitigation strategy of microgrid is developed in the secondary control level, and small signal model of grid-connected microgrid is established to investigate the resonance phenomenon. Simulation and experimental results show that the proposed hierarchical control framework is able to perform active thermal management, improve operation efficiency, and mitigate harmonic resonance in either autonomous mode or grid-connected mode. The proposed hierarchical control framework is an enhanced complementary for conventional hierarchical control of microgrids.