Extensive nonequilibrium molecular dynamics simulations were carried out to study the transport and separation of binary mixtures of and n-alkane chains in a molecular pore network model of nanoporous carbon molecular-sieve membrane. Separation of both sub- and supercritical mixtures was studied. The membrane was generated atomistically by the Voronoi tessellation of the space, using tens of thousands of atoms. The simulations indicate that there is an optimal pressure drop for separation of mixtures of and n-alkanes, when the mixtures enter the membrane under supercritical conditions. In addition, separation of from n-alkanes becomes increasingly more efficient as the size of the alkane increases.