The elimination of small and potentially toxic boron species in water is always a significant challenge for conventional membrane technologies. In this study, facile intercalation and functionalization of β-cyclodextrin (CD) onto layered double hydroxides (LDHs) have resulted in the formation of accessible hydroxyl functional groups and anions that exhibit strong sorption and host–guest interaction with boron. Through meticulous molecular design and optimization, the modified LDH possessing the maximum boron adsorption capacity of 96.1 mg g⁻¹ was employed to fabricate a polyamide-based thin-film nanocomposite (TFN) membrane with a loading of 0.10 wt. %. This resultant membrane displayed a high salt rejection and water permeance of 99.4 % and 2.68 LMH bar⁻¹ for brackish water, respectively, which can be attributed to the increased interlayer spacing of 1.67 nm and the thinner selective layer. The innovative TFN membrane also achieved a high boron rejection of 82.3 % against brackish water containing 2,000 mg L⁻¹ NaCl and 15 mg L⁻¹ B at pH 8. This pioneering study provides valuable insights into the design of brackish water reverse osmosis (BWRO) membranes, through the synergistic use of macrocyclic molecules and inorganic layered nanomaterials, that could potentially revolutionize water reuse and boron removal applications.