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The advantages of thin film nanocomposite reverse osmosis (TFN-RO) membranes have been demonstrated by numerous studies within the last decade. This study proposes a facile and novel method to tune the microscale and nanoscale structures, which has good potential to fabricate high-performance TFN-RO membranes. This method involves the addition of alkyl capped silica nanoparticles (alkyl-silica NPs) into the organic phase during interfacial polymerization (IP). We discovered for the first time that the high concentration alkyl-silica NPs in organic solvent isopar-G can limit the diffusion of MPD molecules at the interface, therefore shaping the intrinsic thickness and microstructures of the PA layer. Moreover, the alkyl group modification greatly reduces the NPs agglomeration and increases the compatibility between the NPs and the PA matrix. We further demonstrate that the doping of alkyl-silica NPs impacts the performance of the TFN-RO membrane by affecting intrinsic thickness, higher surface area, hydrophobic plugging effect, and higher surface charge by a series of characterization. At brackish water desalination conditions (2000 ppm NaCl, 1.55 MPa), the optimal brackish water flux was 55.3 L/m²∙h, and the rejection was maintained at 99.6%, or even exceeded this baseline. At seawater desalination conditions (32,000 ppm NaCl, 5.5 MPa), the optimized seawater flux reached 67.7 L/m²∙h, and the rejection was sustained at 99.4%. Moreover, the boron rejection was elevated by 11%, which benefits from a hydrophobic plugging effect of the alkyl groups. Full article