In this study, thin film nanocomposite (TFN) membranes were prepared by incorporating multi-walled carbon nanotube-titania nanotube (MWCNT-TNT) hybrid into the polyamide layer via interfacial polymerization on the surface of PS35 commercial substrate. The study showed that in the neat thin film composite (TFC), the presence of PIP in polyamide layer increased the water permeability (from 0.54 to 2.25 L/m2 h bar) but decreased the NaCl rejection (from 86.48 to 47.45%). Interestingly, the presence of MWCNT-TNT in MPD-PIP polyamide layer increased the NaCl rejection by 38.68% (47.45 to 86.13%) while giving a significant water permeability performance at 0.86 L/m2 h bar. The incorporation of acid treated MWCNT-TNT has improved the water permeability from 0.86 to 0.89 L/m2 h bar while decreasing the NaCl rejection from 86.13 to 77.51%. Further investigation of MWCNT-TNT loading at pH 2 revealed that the increase of its loading in polyamide layer decreased both water permeability and NaCl rejection performance of the membrane. Overall, it can be concluded that the addition of an appropriate loading of surface modified MWCNT-TNT into the polyamide layer can remarkably improve the performance of conventional TFC membranes for desalination applications. In addition, incorporating PIP in the polyamide layer reduces the capability of the membrane on NaCl rejection.