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The surface wettability effect on fluid transport in nanoscale slit pores is quantitatively accessed by using non-equilibrium molecular dynamics (NEMD) simulation incorporating with density functional theory (DFT). In particular, the slip lengths of benzene steady flows under various wetting conditions are computed with NEMD simulations and a quasi-general expression is given, while the structural properties are investigated with DFT. By taking into account the inhomogeneity of fluid density inside pore, we find that the conventional flux enhancement rate is associated with both the molecule slipping and geometrical confinement, and it becomes drastically high in solvophobic pores especially when the pore size is of several fluid diameters. In good agreement with experimental results, we further show that the wettability effect competes with pore size effect in determining the flux after pore inner surface modification, and a high flux can be achieved when the deposited layer is solvophobic yet thin. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1704-1714, 2017 [ABSTRACT FROM AUTHOR]