Two-dimensional (2D) hexagonal boron nitride (h-BN) has attracted great interest due to its excellent chemical and thermal stability, electrical insulating property, high proton conductivity, and good flexibility. Integration of 2D h-BN into commercial proton exchange membranes (PEMs) has the potential to improve ion selectivity while maintaining the proton conductivity of PEMs simultaneously, which has been a longstanding challenge in membrane separation technology. Until now, such attempts are only limited in mechanically exfoliated small area h-BN and in proof-of-concept devices, due to the difficulty of growing and transferring large area uniform h-BN monolayers. Here, we develop a space-confined chemical vapor deposition approach and achieve the growth of wafer-scale uniform h-BN monolayer films on Cu rolls. We further develop a Nafion functional layer assisted transfer method which effectively transfers as-grown h-BN monolayer films from the Cu roll to sulfonated poly(ether ether ketone) (SPEEK) membrane. The as-fabricated Nafion/h-BN/SPEEK sandwich structure is used as the membrane and compared with the pure SPEEK membrane for flow batteries. Results show that the sandwich membrane exhibits ion selectivity 3-fold greater than that of a pure SPEEK membrane ( i.e., 32.1 × 104 vs 9.7 × 104 S min cm-3). In addition, we fabricate vanadium flow batteries using the Nafion/h-BN/SPEEK sandwich membrane and find that the sandwich structure does not affect the proton transport but inhibits vanadium crossover at low current density (<120 mA cm-2) due to the selective blocking of vanadium ions by 2D h-BN. As a result, the sandwich membrane exhibits a significantly improved Coulombic efficiency and energy efficiency, ∼95% and ∼91%, respectively. Our results suggest that a functional layer/2D film/target substrate-based sandwich structure shows clear potential for future 2D material-based membranes in separation technologies.