Based on a mutual internal relationship among membrane properties (e.g., permeability, selectivity, antifouling ability), a comprehensive performance improvement of the thin film composite (TFC) membrane remains the huge issue. In this study, single walled carbon nanotube (SWCNT) was used as a nanofiller to tune the polyester membrane via the IP reaction with carboxymethyl cellulose (CMC) and TMC as aqueous and organic monomer, respectively. Through Van der Waals interaction and hydrogen bonding with SWCNT, the diffusion behavior of CMC towards the TMC boundary was affected and finally tune the properties and structures of the polyester active layer. Besides, physical and chemical natures of the fabricated membranes modified by different SWCNT concentrations were characterized. The results revealed that polyester selective layer presented a rougher and more hydrophilic surface with an increased content, which were beneficial for water molecules transit. Consequently, the optimal TFC membrane decorated by 0.50 mg SWCNT presented an excellent permeance at 14.47 L m−2 h−1 bar−1 and satisfied dye retention of 99.7%, 100.0%, 100.0%, and 98.0% for congo red, coomassie blue G250, reactive blue 19, and methyl blue, respectively. Moreover, TFC membrane exhibited moderate salt rejections against Na2SO4 (91.8%), MgSO4 (23.2%), NaCl (24.3%), and MgCl2 (2.9%) and preferable long-term filtration stability of 72 h, which was rather competitive for the application of wastewater treatment.