In realistic scenarios, the dynamic performance of a microgrid cluster is largely affected by the intermittent power of renewable energy sources and frequent load changes. To address this issue, a distributed fixed-time based dual layer secondary controller is designed to improve inter-microgrid and intra-microgrid dynamic performance within a fixed settling time. The proposed controller is independent of initial operating values as opposed to the finite time control law. Each global agent in a microgrid operates to mitigate loading mismatch between other global agents, whereas each local agent in a microgrid operates to achieve proportionate load current sharing and average voltage regulation between them in fixed time. However, as loading mismatch mitigation during light load conditions affects the system efficiency due to significant line losses, the cluster operation switches to a distributed loss minimization approach, which operates using online measurements from the neighboring microgrids. To characterize the mode of operation in the global cyber layer, a critical point of loading threshold for the cluster is thus determined. The performance of the cluster employing the proposed strategy is simulated in MATLAB/SIMULINK environment for various scenarios to demonstrate its reliability and efficiency.