Abstract Aquaporin water channels enable fast water transport while maintaining the resistance against protons and ions. We mimic this aquaporin with a rigid or flexible hourglass-shaped nanopore in our molecular dynamics simulation. The simulation was non-equilibrium one with applied uniform external forces with the purpose of mimicking osmosis-driven flows. The simplified computational model successfully captures the important physics of real aquaporin to confirm the validity of our flexible hourglass-shaped pore model. We also found that the hourglass-shaped pore has the ability to occupy more water molecules and conduct faster water transport than the straight pores with the pore diameter. We suggest that deforming straight nanopores into hourglass-shape may enhance the ability of water transport in thin membranes.