To achieve greater separation performance and antifouling properties in a thin-film composite (TFC) nanofiltration membrane, cellulose nanocrystals (CNCs) were incorporated into the polyamide layer of a TFC membrane for the first time. The results of Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy (XPS) confirmed the successful formation of the CNC-polyamide composite layer. Surface characterization results revealed differences in the morphologies of the CNC-TFC membranes compared with a control membrane (CNC-TFC-0). Streaming potential measurements and molecular weight cutoff (MWCO) characterizations showed that the CNC-TFC membranes exhibited a greater negative surface charge and a smaller MWCO as the CNC content increased. The CNC-TFC membranes showed enhanced hydrophilicity and increased permeability. With the incorporation of only 0.020 wt % CNCs, the permeability of the CNC-TFC membrane increased by 60.0% over that of the polyamide TFC without CNC. Rejection of Na2SO4 and MgSO4 by the CNC-TFC membranes was similar to that observed for the CNC-TFC-0 membrane, at values of approximately 98.7% and 98.8%, respectively, indicating that divalent salt rejection was not sacrificed. The monovalent ion rejection tended to increase as the CNC content increased. In addition, the CNC-TFC membranes exhibited enhanced antifouling properties due to their increased hydrophilicity and more negatively charged surfaces.