Proton exchange membranes with low methanol permeability are constructed by incorporating Nafion into a covalently cross-linked network composed of 4,4'-methylenedianiline (MDA) and 3-glycidoxypropyltrimethoxysilane (GPTMS) by ionical cross-linking. The robust framework is full of covalently bonded polysiloxane. The association of Nafion with the cross-linked polysiloxane network results from the ionic interaction between the sulfonic acid groups on Nafion and the amine groups next to polysiloxane. Evidence of the interaction is the shift of the XPS spectra in the S 2p region and the -SO3 stretching band at 1057.8 cm(-1) in ATR/FTIR which induced a change of the hydrophilic/hydrophobic microphase separation. The polysiloxane network contributed to the increase in bound water degree, higher proton conductivity at temperatures higher than 70 degrees C, and greatly decreased methanol permeability. The increasing polysiloxane concentration reduces the methanol permeability to 10(-8) cm(2)/s. With a polysiloxane concentration of 15% MG(4), at 30 degrees C, the composite membrane showed both good proton conductivity (i.e., sigma = 3.4 x 10(-2) S/cm) and ultralow methanol permeability (i.e., P = 1.1 x 10(-8) cm(2)/s). The composite performed better than Nafion-117 (sigma = 4.5 x 10(-2) S/cm and P = 2.2 x 10(-6) cm(2)/s) under the same conditions.