As　a　novel　two-dimensional　material,　graphitic　carbon　nitride　(g-C3N4)　has　proved　to　be　promising　for　separation　membrane.　However,　the　assessment　of　nanopomus　g-C3N4　membrane　for　efficient　desalination　process　has　not　been　systematically　investigated　yet.　In　this　work,　we　designed　three　g-C3N4　nanopores　with　different　shapes　based　on　the　membrane　unit　structure.　The　non-equilibrium　molecular　dynamics　simulations　were　used　to　study　the　molecular　mechanism　of　saline　water　permeation　through　the　nanoporous　g-C3N4　membranes.　The　relationship　between　water　flow　rate　and　external　pressure　was　in　good　agreement　with　the　classical　hydrodynamics.　Meanwhile,　we　observed　that　the　local　water　diffusion　coefficient　increased　as　the　enlargement　of　nanopore　sizes,　indicating　that　the　nano-effect　may　also　rule　the　water　permeation.　For　desalination　purposes,　the　designed　g-C3N4　nanopomus　membrane　entirely　rejected　ions　while　maintaining　a　considerable　water　permeability　of　14.9　L/cm(2)/day/MPa.　By　analyzing　the　trajectories　of　ions　passing　through　the　nanopores,　we　found　that　the　configurational　shape　could　divide　one　nanopore　into　several　sub-regions,　and　specific　ones　may　determine　the　desalination　performance　of　the　nanoporous　membrane.　This　work　unveils　the　molecular　insights　into　the　desalination　process　of　nanoporous　g-C3N4　membrane　and　further　provides　useful　guidelines　for　the　design　of　next　generation　desalination　membranes　with　complex　nanopore　structures.