This work presents the design of a new membrane including an array of nano-magnets (magnetic CNTs) as an alternative candidate for efficient O2/N2 separation by using the molecular dynamics (MD) technique. The behavior of the magnetic CNTs is based on the delocalized magnetic moments of transition metal elements which embedded within the CNTs. Hence, the magnetic membrane technology is employed together with the magnetic separation technology for O2/N2 separation; Different responses of paramagnetic oxygen and diamagnetic nitrogen molecules under an applied magnetic field gradient are the basis of the performance of this system. Permeability and selectivity of the membrane are investigated through the involvement of magnetic dipole–dipole and pare-particle Lennard-Jones (L-J) interactions in a constant gas pressure difference on the sides of the membrane. The effects of the multilayering and other design parameters (interlayer distance d, interablock spacing ℓ, slit size s) on the separation performance of MCNTM are investigated. It was found that the separation performance is sensitive to variations in d, ℓ, and s. Furthermore, the influence of the strong or weak magnetic gradient rate and also the temperature are evaluated numerically. Finally, this work provides computational evidence that the magnetic multilayer MCNTM can be used as a high-performance O2/N2 separator, as well as, an oxygen buffer or a temporary storage system at room temperature and 77 K.