Multiwall carbon nanotubes (MWCNTs) are often used to modify polymer membranes as additives, however, MWCNTs are easy to agglomerate and entangle in polymer matrix due to their own strong van der Waals force. MWCNTs were doubly modified by bonding octadecylamine (ODA) and SiO2 through the respective amidation and esterification reactions to prepare SiO2-MWCNT-ODA nanocomposites. The amino groups on ODA were amidated with the carboxyl groups on MWCNT-COOH. Then the hydroxyl groups on SiO2 were bonded to MWCNT-COOH through esterification to obtain SiO2-MWCNT-ODA nanocomposites. PES/SiO2-MWCNT-ODA composite ultrafiltration (UF) membrane was prepared by non-solvent induced phase separation (NIPS) method. SiO2-MWCNT-ODA nanocomposites and PES/SiO2-MWCNT-ODA membrane were characterized by FTIR, XRD, TGA, and SEM, etc. The results showed that PES/SiO2-MWCNT-ODA membrane had significantly improved permeability, rejection, and antifouling properties for comparison with PES membrane. The pure water flux of PES/Nano.2-0.5 reached 212.5 L m−2 h−1, which was approximately 2.6 times than that of PES membrane, and the rejection of BSA protein for composite membrane was as high as 94.2%. PES/SiO2-MWCNT-ODA composite membrane had excellent antifouling performance and the flux recovery rate (FRR) of PES/Nano.2-0.5 membrane could still maintain at higher value of 84.82% after two cycles in the antifouling test.