Clean energy technologies represent a hot topic for research communities worldwide. Hydrogen fuel, a prized alternative to fossil fuels, displays weaknesses such as the poisoning by impurities of the precious metal catalyst which controls the reaction involved in its production. Thus, separating H2 out of the other gases, meaning CH4, CO, CO2, N2, and H2O is essential. We present a rotating partially double-walled carbon nanotube membrane design for hydrogen separation and evaluate its performance using molecular dynamics simulations by imposing three discrete angular velocities. We provide a nano-perspective of the gas behaviors inside the membrane and extract key insights from the filtration process, pore placement, flux, and permeance of the membrane. We display a very high selectivity case (ω = 180° ps−1) and show that the outcome of Molecular Dynamics (MD) simulations can be both intuitive and counter-intuitive when increasing the ω parameter (ω = 270° ps−1; ω = 360° ps−1). Thus, in the highly selective, ω = 180° ps−1, only H2 molecules and 1–2 H2O molecules pass into the filtrate area. In the ω = 270° ps−1, H2, CO, CH4, N2, and H2O molecules were observed to pass, while, perhaps counter-intuitively, in the third case, with the highest imposed angular velocity of 360° ps−1 only CH4 and H2 molecules were able to pass through the pores leading to the filtrate area.