D-amino acid (DAA) an environmentally friendly biofilm inhibitor, has low efficiency for membrane biofouling control due to its instability. To address this challenge, a novel nanocomposite was prepared with DAA adhering to polydopamine (PDA)-coated halloysite nanotube (HNTs) through the interactions of H-bonding and pi-pi stacking between PDA and DAA. Membrane modified with such nanocomposite was fabricated via blending phase inversion, and the nanocomposite was uniformly distributed in the modified membrane matrix. In comparison with the pristine membrane, the addition of nanocomposites resulted in robust mechanical property for modified membrane with the ultimate stress and strain increased by 23.97% and 35.62%, respectively. Moreover, an excellent tradeoff between water flux (2.5 folds of pristine membrane) and selectivity was achieved, probably due to the improved membrane hydrophilicity. Meanwhile, bovine serum protein (BSA) static adsorption as well as dynamic filtration experiments exhibited excellent antifouling ability of the modified membrane. Most importantly, a superior anti-biofouling stability over a 10-day period was obtained for the membrane modified with nanocomposite, indicating that the activity of DAA to mitigate biofouling was effectively maintained. This study developed a novel and promising strategy for membrane biofouling mitigation.