Reverse osmosis (RO) technology is currently the most progressive, energy-saving and efficient membrane separation technology . Meanwhile, graphene becomes a promising candidate for fabricating the RO membranes in water desalination due to its high salt rejection and water flux. The concept of “temporal selectivity” is first proposed in our previous work in terms of the time difference between the penetration time of an ion passing through the pore and the tangential slipping time for the ion sliding across the pore. Nevertheless, the temporal selectivity mechanism of multilayered graphene membrane remains ambiguous. In this paper, the RO process of saltwater through porous graphene column RO membrane is studied by using molecular dynamics (MD) simulations method, and the effects of rotating angular velocity and the thickness of RO membrane on desalination performance of seawater are considered first. The MD results show that the salt rejection increases with the rotation speed of porous membrane increasing while the water flux initially increases and then decreases . Meanwhile, the interfacial slip velocity increases linearly with angular velocity increasing. On the other hand, the increasing thickness of porous graphene membrane can enhance the selectivity and reduce the permeability of water molecules. As expected, the tri-layered porous graphene RO membrane can achieve high salt rejection at low interfacial slip velocity. In order to ensure high selectivity and energy conservation and efficient, the pore structure of the porous graphene RO membrane is optimized. The results show that the optimized nanopores can increase the water flux significantly, whereas the salt rejection is not changed appreciably. It is found that the pore size of the innermost layer membrane near the feed region has the most significant effect on the water flux. The water flux increases sharply with the increase of pore diameter and the salt rejection remains totally higher than 80%. Moreover, the RO membrane with a special Type 3 structure exhibits excellent performance in seawater desalination, specifically, the ultrahigh water flux reaches 20029 L·cm^–2·d^–1 and the super salt rejection arrives at 94%. The research results further clarify and verify the mechanism of the temporal selectivity in RO process, and improve the water flux under the condition of the same membrane thickness by designing gradient hole. The findings can conduce to the in-depth theoretical understanding of porous graphene-based membranes and designing and developing the large-scale seawater desalination devices and water filtration equipment.