Graphene‐based membranes have been shown to exhibit excellent potential in transporting water and separating ions and contaminants. The pressure‐driven water permeation through a graphene (GE) multilayer containing slit‐like gaps in each layer is investigated using molecular dynamics simulations in the present study. The effects of the driving pressure magnitude, as well as the multilayer configuration parameters including the number of GE layers, their porous ratio, the gap width and offset, the interlayer distance, and the hydrogenation of the gaps, are studied. The results show that the permeate flux is highly dependent on the number and the porous ratio of the GE layers, but is almost insensitive to the number of gaps at the same porous ratio as long as the gap width is large enough to allow water permeation. A counter‐intuitive dependence of the water flow rate on the offset distance is found that the former increases as the later increases. When the gaps are hydrogenated, the energy barrier for the water molecules entering the nanochannel is lowered, leading to much higher water flow rate across the membrane. This study is helpful for the application of GE‐based membranes for desalination and nanofiltration.