Abstract The transportation of hydrogen molecules using carbon nanotubes subjected to torsion is studied with molecular dynamics. Molecular dynamics simulations reveal that the transportation in a (10, 0) carbon nanotube is a result of the van der Waals effect through the propagation of the kink initiated at the onset of the tube torsional buckling. In addition, the applied torsional loading rate has an obvious effect on the orientation of the molecular transportation. On the other hand, the motion of the molecules in a (10, 10) carbon nanotube is found to be less oriented. The mechanism of the transportation in the larger carbon nanotube is investigated through the transform of the collapsed wall of the tube in the dynamic process of the torsional buckling.