Innovations in self-assembly and aggregate engineering have led to membranes that better balance water permeability with salt rejection, overcoming traditional trade-offs. Here we demonstrate a strategy that uses multivalent H-bond interactions at the nano-confined space to manipulate controllable and organized crystallization. Specifically, we design amphiphilic oligomers featuring hydrophobic segments with strongly polar end-capped motifs. When spreading on air/water interfaces, the hydrophobic parts repel water, yielding an ordered alignment of supramolecular oligomers under nano-confinement, while the strongly polar sections engage in strong hydrogen bonding and reconfigure to strongly interact with water molecules, enabling the controlled assembly and orientation of nano-confined crystalline domains. This arrangement provides dual benefits: refining the distribution of pore sizes for ultra-selectivity and boosting the free volume for water permeation. Compared to counterpart oligomers with weakly polar motifs, the optimized membrane with a 6-nm thickness demonstrates the water permeability of 14.8 L m