In order to improve the dynamic stability of multi-area microgrid (MG) clusters in the autonomous mode, this study proposes a novel fuzzy-based dynamic inertia control strategy for supercapacitors in multi-area autonomous MG clusters. By virtue of the integral manifold theory, the interactive influence of inertia on dynamic stability for multi-area MG clusters is explored in detail. The energy function of multi-area MG clusters is constructed to further analyze the inertia constant. Based on the analysis of the mechanism, a control strategy for the fuzzy-based dynamic inertia control of supercapacitors for multi-area MG clusters is further proposed. For each sub-microgrid (sub-MG), the gain of the fuzzy-based dynamic inertia control is self-tuned dynamically, with system events being triggered, so as to flexibly and robustly enhance the dynamic performance of the multi-area MG clusters in the autonomous mode. To verify the effectiveness of the proposed control scheme, a three-area photovoltaic (PV)-based MG cluster is designed and simulated on the MATLAB/Simulink platform. Moreover, a comparison between the dynamic fuzzy-based inertial control method and an additional droop control method is finally presented to validate the advantages of the fuzzy-based dynamic inertial control approach.