Surface patterning is a promising strategy to overcome the trade-off effect of separation membranes. Herein, a bottom-up patterning strategy of locking micron-sized carbon nanotube cages (CNCs) onto a nanofibrous substrate is developed. The strongly enhanced capillary force triggered by the abundant narrow channels in CNCs endows the precisely patterned substrate with excellent wettability and antigravity water transport. Both are crucial for the preloading of cucurbit[n]uril (CB6)-embeded amine solution to form an ultrathin (∼20 nm) polyamide selective layer clinging to CNCs-patterned substrate. The CNCs-patterning and CB6 modification result in a 40.2% increased transmission area, a reduced thickness, and a lowered cross-linking degree of selective layer, leading to a high water permeability of 124.9 L·m-2 h-1 bar-1 and a rejection of 99.9% for Janus Green B (511.07 Da), an order of magnitude higher than that of commercial membranes. The new patterning strategy provides technical and theoretical guidance for designing next-generation dye/salt separation membranes.