Engineering different two-dimensional materials into heterostructured membranes with unique physiochemical properties and molecular sieving channels offers an effective way to design membranes for fast and selective gas molecule transport. Here we develop a simple and versatile pyro-layering approach to fabricate heterostructured membranes from boron nitride nanosheets as the main scaffold and graphene nanosheets derived from a chitosan precursor as the filler. The rearrangement of the graphene nanosheets adjoining the boron nitride nanosheets during the pyro-layering treatment forms precise in-plane slit-like nanochannels and a plane-to-plane spacing of ~3.0 Å, thereby endowing specific gas transport pathways for selective hydrogen transport. The heterostructured membrane shows a high H2 permeability of 849 Barrer, with a H2/CO2 selectivity of 290. This facile and scalable technique holds great promise for the fabrication of heterostructures as next-generation membranes for enhancing the efficiency of gas separation and purification processes.