Nanofiltration (NF) technology is attractive in desalting and concentrating dyeing wastewater in the textile industry. A highly efficient NF membrane is critical in reducing the cost of the process. Here, a facile and reliable approach to prepare an NF membrane for the selective separation of dye/salt is proposed by surface grafting of 3-aminopropyltriethoxysilane (APTES) on a fresh polyamide (PA) layer after interfacial polymerization (IP). A thin layer of APTES with a thickness of ∼64 nm was found successfully covalently bonded onto the PA surface via esterification and amidation reactions. The thin-film composite (TFC)-1.0 membrane grafted with 10% APTES achieved a high water permeance of 44.8 L m–2 h–1 bar–1, which was 4.7 times higher than that of the control TFC membrane. Interestingly, the rejection of monovalent salt (NaCl, 11.5%) and divalent salt (Na2SO4, 17.2%) decreased significantly, while the rejection for different dyes (Congo red, reactive blue-19, Coomassie blue G-250, and methyl blue) remained over 99.0%. These noticeable changes in separation performances could be attributed to the large pore size of the active layer, resulting from the interference of APTES on the post-cross-linking of a PA network. The poly(ethylene glycol) (PEG) filtration experiments confirmed that the mean pore size of the membrane was enlarged significantly from 0.51 to 1.17 nm after surface modification. Finally, the modified membrane showed good long-term stability and excellent separation efficiencies in fractionation of a high salinity Congo red/NaCl (0.2/50 g L–1) mixture. Overall, this work provides a practical strategy to prepare a permeable and selective NF membrane for dye and salt separation by surface grafting of the nascent PA layer.