Helium is usually recovered from natural gas, which is mainly consisted of methane (CH4). In this work, we investigated the ability of the SIFSIX-3-Cu membrane for separating of helium (He) gas from He/CH4 mixed gas using molecular dynamics (MD) simulation. Herein, we studied the impact of system temperature (298, 323, and 348 K), applied pressure gradient (up to 3 MPa), and feed concentration on the He/CH4 separation performance. It is found that the SIFSIX-3-Cu membrane can fulfill both the high selectivity and permeance for He separation and surpass Robeson's upper bound by preparing the maximum He permeance of 1.64 x 106 GPU and an ul-trahigh selectivity of He over CH4 molecules, which confirms the high productivity of the membrane in recovery of He from binary gas mixture. For further study of the gas molecules permeation through the membrane, the van der Waals interactions, z-position, potential of the mean force calculations, density map, and density profile were conducted. It is exhibited that adsorption favors CH4 gas molecules on the SIFSIX-3-Cu membrane surface, while diffusion prefers He. The results suggested that the SIFSIX-3-Cu membrane can be an appropriate candidate for the separation of He from He/CH4 gas mixture.