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Abstract Graphene-based electrodes have been extensively investigated for supercapacitor applications. However, their ion diffusion efficiency is often hindered by the graphene restacking phenomenon. Even though holey graphene is fabricated to address this issue by providing ion transport channels, those channels could still be blocked by densely stacked graphene nanosheets. To tackle this challenge, this research aims at improving the ion diffusion efficiency of microwave-synthesized holey graphene films by tuning the water interlayer spacer towards the improved supercapacitor performance. By controlling the vacuum filtration during graphene-based electrode fabrication, we obtain dry films with dense packing and wet films with sparse packing. The SEM images reveal that 20 times larger interlayer distance is constructed in the wet film compared to that in the dry counterpart. The holey graphene wet film delivers a specific capacitance of 239 F/g, ~82% enhancement over the dry film (131 F/g). By an integrated experimental and computational study, we quantitatively show that the interlayer spacing in combination with the nanoholes in the basal plane dominates the ion diffusion rate in holey graphene-based electrodes. Our study concludes that novel hierarchical structures should be further considered even in holey graphene thin films to fully exploit the superior advantages of graphene-based supercapacitors.