In this study, the carbon nanotubes (CNTs) are successively coated via sol-gel method with SiO 2 (SiO 2 @CNTs), followed by grafting with 3-merraptnpropyltrimethnxysilane and oxidation with hydrogen peroxide to yield dual-modified CNTs (SSiO 2 @CNTs). The SSiO 2 @CNTs material is applied to prepared chitosan (CS) based composite proton exchange membranes by the incorporation of various content of SSiO 2 @CNTs, the structure and properties of as-prepared composite membranes are fully investigated. Compared to pristine CS membrane, the SSiO 2 @CNTs-filled composite membranes show improved thermal stability, mechanical stability, and methanol resistance, owing to the effective interface interaction and good compatibility between SSiO 2 @CNTs and CS matrix. Additionally, the doping of SSiO 2 @CNTs also generates a positive effect on the electrochemistry performance, due to the construction of abundant transport channel and providing more proton sources or proton sites. Particularly, the CS/SSiO 2 @CNTs-7 membrane exhibits tensile strength of about 40.1 MPa and proton conductivity of 35.8 mS cm −1 at 80 °C, which is almost 1.6 and 2.0 times higher than pure CS membrane, and lower methanol permeability of 0.9 × 10 −6 cm 2 s −1 . The direct methanol fuel cell performance (DMFC) of CS/SSiO 2 @CNTs-7 membrane is also improved with open circuit voltage of 0.67 V and maximum power density of 60.7 mW cm −2 at 70 °C.