Thin film nanocomposite (TFN) membranes have shown remarkable potential for the extensive application in various areas, such as industrial and domestic wastewater treatment, dye desalination, and chemicals separation and purification. This work proposes a highly efficient TFN membrane by incorporation of the amine-functionalized ordered mesoporous silica (APTES-SBA-15) nanoparticles into the polyvinyl alcohol (PVA) top layer of a polyvinylchloride (PVC)-based membrane. The superior TFN membranes were fabricated through a facile and optimum preparation method consisting of immersion-precipitation phase inversion followed by dip-coating method to address the challenges hindering performance. The physicochemical characteristics of the synthesized nanoparticles and prepared TFN membranes were studied using a variety of techniques including XRD, FTIR, AFM, FE-SEM and contact angle measurements. The presence of APTES-SBA-15 nanoparticles in TFN membrane enables efficient separation of contaminants compared to pure thin film composite (TFC) and SBA-15 TFN membranes that were investigated by calculating the values of various parameters such as water flux, flux recovery ratio (FRR), rejection percentage, total fouling ratio (TFR), and irreversible fouling ratio (IFR). A more hydrophilic TFN membrane containing 0.50 wt% APTES-SBA-15 nanoparticles (M3 membrane) exhibits a rejection performance of 91.41%, TFR value of 88.89% and IFR value of 11.11% with a total organic carbon (TOC) content of 15.05 mg/L for the treatment of petroleum refinery wastewater.