The aim of this study was to remove Azo dye, Direct Red 16, from a synthetic solution, 50 mg/l, and also to treat the wastewater of the licorice extract plant, LEP, by nanofiltration membrane with high anti-fouling properties. In this regard, a new polymer nanocomposite was fabricated by mixing cellulose nanocrystals functionalized with amino acid cysteine (CNF-AAC) and investigating the effective parameters such as anti-fouling properties, as well as the performance of the modified membrane in removing the dye. In this regard, field emission scanning electron microscopy (FESEM), scanning-force microscopy (SFM), atomic force microscopy (AFM) and contact angle measurements were performed. The results of AFM analysis indicated that the surface roughness of polyether sulfone-membrane is reduced by the addition of CNF-AAC. Therefore, by increasing the concentration of nanocrystals from 0 to 1 wt% in the initial solution of the membrane, the net distilled water flux permeation has increased from 18.05 (kg/m2h) to 26.50 (kg/m2h). Also, with increasing the concentration of CNF-AAC in the initial solution of the membranes, the size of the contact angle has gradually decreased. Meanwhile, adding a small amount of CNF-AAC (0.5 wt%) to the polyether-sulfone membrane has led to reducing the rate of irreversible fouling from 43.34% to 4.89% and in contrast, to increasing the amount of reversible fouling from 30.02% to 63.54%. On the other hand, in this study, the yield of dye solution by the optimal membrane is 98.38%, for which the percentage of COD removal for the wastewater of LEP has reached 90%.