Two-dimensional materials provide an ideal platform for studying the fundamental properties of atomic-level thickness systems, and are appropriate for lots of engineering applications in various fields. Although 2D materials are the thinnest membranes, they have been revealed to have high impermeability even to the smallest molecule. By the virtue of this high impermeability of the 2D materials in combination with their other unique properties, 2D materials open up a variety of applications that are impossible for conventional membranes. In this review, the latest applications based on high impermeability and selective permeation of these 2D material membranes are overviewed for different fields, including environmental control, chemical engineering, electronic devices, and biosensors. The working mechanism for each kind of application is described in detail. A summary and outlook is then provided on the challenges and new directions in this emerging research field.