Hydrogen isotope separation has been effectively achieved electrochemically by passage of gaseous H2/D2 through graphene/Nafion composite membranes. Nevertheless, deuteron nearly does not exist in the form of gaseous D2 in nature but as liquid water. Thus, it is a more feasible way to separate and enrich deuterium from water. Herein, we have successfully transferred monolayer graphene to a rigid and porous polymer substrate, PITEM (polyimide track-etched membrane), which could avoid the swelling problem of the Nafion substrate as well as keep the integrity of graphene. Meanwhile, defects in the large area of CVD graphene could be successfully repaired by interfacial polymerization resulting in a high separation factor. Moreover, a new model was proposed for the proton transport mechanism through monolayer graphene based on the kinetic isotope effect (KIE). In this model, graphene plays a significant role in the H/D separation process by completely breaking the O-H/O-D bond, which can maximize the KIE, leading to increased H/D separation performance. This work suggests a promising application for using monolayer graphene in the industry and proposes a pronounced understanding of proton transport in graphene.