The invention discloses a multi-aperture graphene film manufacturing method. In the method, an energy beam is used for radiating the graphene film with lattice imperfection, as a result, the carbon bonding with lattice imperfection in graphene carbon ring hexagonal structure is broken, aperture is generated, and the multi-aperture graphene film is generated; moreover, size of the aperture is controlled by regulation on concentration of the lattice imperfection and/or radiation intensity of the energy beam. The invention further discloses a gas separation element using the multi-aperture graphene film manufactured by the method. By the method, the graphene film with gas permeation aperture is prepared actually for the first time, and application of the graphene film in the aspect of gas separation is realized successfully; in the method, size of aperture can be controlled as needed, moreover, the preparation technology is simple, the implementation cost is low, so that the method is suitable for large-scale industrial application; the gas separation element provided by the invention has very strong selectivity and high permeability to gas molecules, and by experimental verification, separation coefficient of the gas separation element to H2/N2 at normal temperature is up to 260.