The purity of hydrogen, a renewable and efficient clean energy, has to be guaranteed in industry production. Membrane separation technology is an efficient approach. Herein, the hydrogen purification performance in a new type graphene-like carbon nitride (C₉N₄) membrane has been investigated by using density functional theory (DFT) and molecular dynamics (MD) simulation. Results of DFT calculations showed that gases were physically adsorbed on C₉N₄ membrane. C₉N₄ membrane exhibited considerably high permeability and excellent selectivity for H₂. The permeance of H₂ reached 1.89×10 ^-5mol·m ^-2·s ^-1·Pa ^-1, and the selectivity of H₂/CH₄ reached 10 ²⁴ at 300 K. Results of MD simulations also demonstrated that C₉N₄ membrane exhibited good hydrogen separation performance.