Because of the high water flux and excellent ion rejection, the pores graphene is considered as a promising candidate material for fabricating the membranes in reverse osmosis (RO) process. Unfortunately, water molecules cannot pass through the perfect graphene, and how to effectively create a large number of nanopores with controllable size remains a challenge, which seriously prevents the practical application and development of graphene membrane for desalination. Recently, the emergence of pillared graphene (PGN) might open a new way for designing the graphene-based membranes, which can compensate for the deficiency of porous graphene membrane. The PGN has been extensively studied in gas storage and separation, and its RO characteristics and mechanism still remain unclear because the limitation of large area preparation in desalination. In this paper, the RO process of seawater through PGN membranes is investigated by molecular dynamics simulations, and the influences of the pressure within feed solution, temperature and the shearing of membrane on the desalination properties are considered. It is found that the water flux increases linearly with the pressure within feed solution increasing, and the PGN membrane with nanopore diameter of 0.8 nm can conduct water molecules but completely rejects high-concentration ions. As the diameter of nanopores increases to 1.2 nm, the rise of temperature can increase the permeability of water molecules, whereas the salt rejection is not appreciably sensitive to the temperature. Particularly, the shearing membrane can improve the salt rejection and hinder the water molecules from permeating at the same time. The designed PGN membrane exhibits excellent performance of water purification, and the ultrahigh water flux obtained in this work reaches 56.15 L·cm ^–2·day ^–1·MPa ^–1with a salt rejection of 88.9%. Subsequently, the hydrogen bond dynamics is calculated in order to explain the variation of water permeability under different conditions. The result shows that the rise of temperature reduces the stability of hydrogen bonds and leads the water flux to increase, while the increase of shearing speed will enhance the stability of hydrogen bonds and inhibit water seepage. Furthermore, the analysis results of hydrogen bond and ionic hydration structure show that the shear motion on RO membrane will improve the stability of ionic hydration shell, which makes it more difficult for the ions to pass through nanopores by weakening the hydration shell. On the contrary, rising temperature will impair the strength of ionic hydration shell, leading more ions to pass through the RO membrane. The simulation results can provide an in-depth understanding of the desalination performance of PGN membrane under different key conditions, and further demonstrate the promising applications of graphene-based membrane in water desalination.