Deuterium water (D2O) is a strategic material that is widely used in and scientific research and has applications in fields such as nuclear energy generation. However, its content in natural water is extremely low. Therefore, the development of a room‐temperature technology for achieving simple, efficient, and low‐cost separation of D2O from natural water is challenging. In this study, porous graphene (PG) nanosheets with “crater‐like” pores are sandwiched between two layers of graphene oxide (GO) membranes to prepare a GO/PG/GO membrane with a macroscopic heterostructure, which can be used to separate D2O and H2O by pressure‐driven filtration. At 25 °C, the rejection rate of D2O is ≈97%, the selectivity of H2O/D2O is ≈35.2, and the excellent performance can be attributed to the difference of transmembrane resistance and flow state of H2O and D2O in the confinement state. In addition, the D2O concentration in natural water is successfully enriched from 0.013% to 0.059% using only one stage, and the membrane exhibits excellent structural and cycling stability. Therefore, this method does not require ultralow temperatures, high energy supplies, complex separation equipment, or the introduction of toxic chemicals. Thus, it can be directly applied to the large‐scale industrial production and removal of D2O.