By intercalating citrate anions into the inter-layer of layered double hydroxides (LDHs), the inter-layer spacing of the resultant CA-Mg-LDH is enlarged from 7.5 to 11.8 Å. With the aid of this newly developed CA-Mg-LDH, novel thin-film nanocomposite (TFN) membranes have been prepared, systematically investigated, and demonstrated for brackish water reverse osmosis (BWRO) desalination. By manipulating the nanofiller concentration, a water permeance of 3.21 LMH bar−1 and a salt rejection of 98.9% are obtained for the TFN membrane at the optimal loading of 0.15 wt%. It achieves a 68% higher water permeance than the pristine TFC membrane but without notably sacrificing the selectivity, owing to the moderate enlargement of the inter-layer spacing of CA-Mg-LDH. In addition, this novel TFN membrane has a boron rejection of 75% when using a 2000 ppm NaCl solution containing 10 ppm boron as the feed at 20 bar. This work is the first attempt to use CA-Mg-LDH as nanofillers in TFN membranes for demonstration of BWRO and boron removal, offering new insights and strategies for the design of next-generation TFN membranes for water treatment.