Given the global challenge of freshwater scarcity, the importance of seawater desalination technology has grown. This study examines the efficiency and role of hydrophilic-modified covalent organic framework (COF) membranes in seawater desalination through molecular simulations. Incorporating hydrophilic groups like -SO3H into N2COF membranes and optimizing their structure significantly improved water permeability and salt ion retention. Non-equilibrium molecular dynamics (NEMD) simulations showed that hydrophilic modifications enhance water permeability while preserving salt ion interception efficacy. Furthermore, adjusting the membrane's stacking method could further enhance its seawater desalination performance. The simulations confirm the high-efficiency desalination capability of hydrophilic-modified COF membranes and offer crucial theoretical guidance for designing and preparing high-performance desalination materials.