Water permeation is an important issue in both fundamental research and industrial applications. In this work, we report a novel strategy to realize the controllable water permeation on the mixed thiol (containing both alkyl and carboxylic acid groups) modified nanostructured copper mesh films. For acidic and neutral water, the film is superhydrophobic, and the water cannot permeate the film because of the large negative capillary effect resulting from the nanostructures. For basic water, the film shows superhydrophilic property, and thus the water can permeate the film easily. The permeation process of water can be controlled just by simply altering the water pH. A detailed investigation indicates that nanostructures on the substrate and the appropriate size of the microscale mesh pores can enhance not only the static wettability but also the dynamic properties. The excellent controllability of water permeation is ascribed to the combined effect of the chemical variation of the carboxylic acid group and the microstructures on the substrate. This work may provide interesting insight into the new applications that are relevant to the surface wettability, such as filtration, microfluidic device, and some separation systems.