Porous membranes with numerous pores on membrane surface and vertical inner transfer paths display fast molecular transport. Molecules need drill into confined pores on membrane surface primarily and then transfer in inner nanochannels, but the underlying molecule-scale transfer mechanism on surface pores remains unclear. Herein, porous membranes with ultra-thin (12 nm) surface layers which contain uniform pores (∼ 0.6 nm) and adjustable groups on pore rim, and large-pore (2.0 nm) support layers are designed based on MOF and COF materials, respectively. Based on these MOF-on-COF hierarchical membranes, it is demonstrated that polar solvents exert strong interactions with hydroxyl groups on MOF pore rims, which induces an orientated configuration when drilling into pores. And the orientation state becomes more uniform with the increase of hydroxyl group amount and molecular dipole moment. Such orientation generates large intermolecular gaps and thus low transfer resistance. Particularly, the acetonitrile permeance reaches 134 L m−2 h−1 bar−1, ∼ 2 times of that of MOF pores with no hydroxyl group. In contrast, nonpolar molecules display a disordered configuration due to the weak pore-molecule interactions, resulting in different transfer behaviors. Besides, the prepared MOF-on-COF membranes exhibit favorable structural and operational stability.