<p>Two-dimensional (2D) crystals with atomic-level thickness dramatically shorten the gas transport pathways, rendering it exceptionally promising for separation membrane applications. While defect-free 2D crystals such as graphene have long been considered impermeable to all gases, recent studies show that pristine monolayer graphene permits room-temperature hydrogen permeation. However, the identity of the permeating species and its generalizability to other 2D materials remain unclear. Herein, we report hydrogen permeation behavior through varying 2D crystals at elevated temperature, and the hydrogen permeability of graphene can reach up to 10¹⁷s⁻¹m⁻² as the form of protons. This process is evidenced by three critical steps: 2D crystals-assisted catalytic dissociation of hydrogen into protons, protons permeation through the 2D crystals lattice, and proton recombination after permeation. Interestingly, the activation energy remains invariant with the layer number of 2D crystals, but the permeability and activation energy can be modulated by the type of materials, adsorbed metal nanoparticles, and the external atmosphere. These findings reveal a catalysis-driven proton permeation mechanism, and fundamentally deepen the understanding of hydrogen permeation through 2D crystals.</p>