Lamellar membranes are promising for highly selective permeation, among which graphene-based ones are widely studied. However, graphene-based membranes give limited molecule permeance due to the unfavorable microenvironments of nanochannels, mainly single chemical affinity and narrow channel size. Herein, quantum dots (QDs) were introduced into nanochannels to manipulate the microenvironments for optimized performance. Particularly, hydrophobic graphene quantum dots were anchored in hydrophilic graphene oxide nanochannels to improve the affinity towards nonpolar molecules and locally enlarge the channel size from 0.84 to 1.35 nm. The pleasant affinity facilitates rapid dissolution and entry of molecules into nanochannels, and the enlarged channel size promotes their fast transport. This synergistic effect permits remarkably enhanced permeance for both polar and nonpolar molecules, especially for nonpolar ones. Meanwhile, the narrow distance at QD-free area effectively rejects dyes larger than 2.0 nm. Additionally, the strong covalent bonds between QDs and adjacent nanosheets bring superior stability for membranes.