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Summary: Graphene and its hybrids have been considered promising candidates for electrochemical energy storage because of their fascinating physicochemical properties. However, they suffer from unsatisfactory areal or volumetric energy density and relatively poor rate performance. These drawbacks are due to limited accessible surface area and poor ion diffusion capacity arising from the agglomeration and restacking of graphene nanosheets during electrode assembly. To solve the above issues, perforation on the graphene planes is adopted, which bestows the graphene-based nanomaterials with porous architectures. In particular, in-plane holes are capable of accelerating ion transport across the graphene sheets and ultimately accessing the inner electrode surface. Here, a comprehensive review of holey graphene-based nanomaterials is presented, which summarizes recent progress from their rational design and controlled synthesis to their applications in electrochemical energy storage. Finally, perspectives on the future directions of their large-scale synthesis and advanced assembly protocols as electrodes are proposed and discussed.