Amine functionalized solids demonstrate well potential in CO2 capture, but this modification may affect the potential water storage capacity of zeolites that possess natural interlinked channels. This study systematically examined the wetting characteristics of droplets on ZSM-5 [0 0 1] surfaces with amino silane modifications and structural water adsorption behaviors using molecular dynamics simulations. The interaction mechanisms between water molecules and particles within the structure were analyzed, and droplet wetting and penetration modes were proposed. The hydrophobicity enhanced by modified surfaces effectively decelerated the wetting process. Nevertheless, water molecules continued to penetrate the zeolite structure via surface cavities, albeit in reduced numbers as coverage increases. N atoms in the amino groups attracted water molecules to form weak hydrogen bond networks, and under the intrinsic driving forces of water molecules and competitive adsorption site occupation, the wetting and permeation processes of droplets were facilitated. Amine functionalized membranes reduced water flux during the membrane separation process, while high-concentration group modification achieved complete ion rejection. Deciphering the wetting and water transport mechanisms within the structure of zeolites and their modified surfaces at the molecular level aids in balancing the requirements of surface hydrophilicity and hydrophobicity along with structural water flux.