In this work, the seawater desalination performance of carbon honeycomb (CHC) membrane via the pervaporation (PV) process is investigated by molecular dynamics simulations. The simulation results show that the CHC membrane can lead to superior evaporation water flux with complete salt rejection. Unintuitively, the evaporation water flux first increases and then decreases with the increase of membrane thickness, showing a nonmonotonic dependence. Detailed analysis of the density distribution and diffusion dynamics of the water molecules indicates that this nonmonotonic dependence is closely related to the density gradient in the vapor phase, backward diffusion of evaporated water molecules, and flow resistance of the liquid phase. Increasing the pore size of the CHC membrane can lead to a significant increase in the evaporation water flow. However, an excessively large pore size permits the permeation of Na⁺ and Cl⁻ ions into the CHC membrane, which impedes the diffusion of water molecules and slows down the increasing trend. With the increase in temperature, the evaporation water flux increases as expected because the change in Gibbs free energy becomes increasingly negative. Overall, this work provides insights into the PV performance of CHC membranes and promotes their application in next-generation PV membranes.