Abstract: Shale oil reservoirs are characterized by extremely complex structures and highly distributed nanopores, where fluid transport behaviors deviate significantly from the conventional Darcy’s law. Understanding the transport mechanisms of fluids confined at the nanoscale is therefore of great importance for accurately predicting shale oil recovery. In this study, we investigate the fundamental mechanism of fluid migration in nanopores using two-dimensional nanoporous structures, with particular emphasis on the coupled effects of pore structure scale and wettability on the micro-/nano-scale flow dynamics of water and oil system. To overcome the limitations of conventional models in capturing nanoscale effects with two-dimensional porous structures, a revised planar model for liquid transport in nanochannels is derived. This analysis highlights the substantial deviations in traditional volume-averaging approaches, which fails to properly represent flow physics under nanoscale confinement. Building on the new theoretical framework, a lattice Boltzmann method (LBM) is developed that explicitly incorporates two critical nanoscale effects: viscosity variations in the adsorbed fluid layer and velocity slip at the solid boundaries. This model enables a comprehensive examination of how pore size and contact angle jointly regulate the transport dynamics of fluids in nanoporous media. The simulation results revealed that viscosity variations within the adsorbed layer and velocity slip at the walls give rise to pronounced nanoscale effects, which gradually diminish as the channel size increases. Moreover, notable differences are observed under varying wettability conditions, underscoring the critical role of contact angle in controlling water/oil displacement mechanisms. Specially, strong hydrophilic conditions favor preferential water occupation of narrow pores, whereas hydrophobic conditions enhance oil continuity. Finally, a nanoscale transport regime map is constructed based on structural size and contact angle, offering a systematic framework to evaluate the interplay between nanoscale effects and wettability. This study provides important theoretical insights into fluid transport in nanoporous shale reservoirs and establishes a reference for developing cross-scale transport models in complex geological formations, ultimately contributing to improved strategies for shale oil exploitation.