The primary challenge faced by thin film nanocomposite (TFN) membrane in nanofiltration (NF) process is to effectively resolve the trade-off effect between permeability and selectivity. Herein, a polyamide (PA) TFN membrane with enhanced NF performance was prepared through in-situ interfacial polymerization (in-situ IP) method, using piperazine (PIP) and 3-diamino-methyl-cyclohexyl triethoxysilane (DTES) as co-amine monomers to undergo a reaction with 1,3,5-benzenetricarbonyl trichloride (TMC). This study investigated the effects of DTES on the surface chemical composition, morphologies, hydrophilicity, separation efficiency, and anti-fouling properties of the novel DTES/PIP/TMC TFN membranes. It was found that SiO2 nanoparticles were generated in-situ from the reacted DTES through hydrolysis and self-condensation, resulting in their uniform distribution within the formed PA selective layer with high compatibility and without aggregation. The optimal PA TFN membrane was achieved by adjusting the ration of Si-OH group in formed SiO2 nanoparticles through varying the concentration of DTES concentration. Meanwhile, the induction of SiO2 into the PA layer resulted in an enlargement in membrane pore size and improved surface hydrophilicity. When the concentration of added DTES was 0.333 wt%, the optimal PA TFN membrane (TFN-4) exhibited the highest quantity of formed Si-OH groups, resulting in the excellent performance, including a markedly enhanced water permeability flux of 76.8 L·m−2·h−1 (2-fold larger than that of the pure TFC membrane), a great Na2SO4 rejection of 97.5 %, and a superior Cl−/SO42− permeation selectivity of 46.0. Moreover, the TFN-4 membrane exhibited exceptional stability and superior antifouling properties attributed to its unparalleled hydrophilicity. This work provided a strategy for preparing uniform and high-performance TFN membranes.