Low methanol permeability of proton exchange membranes (PEMs) is greatly important for direct methanol fuel cells (DMFCs). Here, sulfonated poly(ether ether ketone) (SPEEK) based semi-interpenetrating polymer networks (semi-IPNs) are successfully prepared by interpenetrating SPEEK into the in-situ synthesized crosslinking networks. The polymeric networks are formed by the covalent bonds between bromobenzyl groups of bromomethylated poly(phenylene oxide) and amine groups of diamine linkers as well as the ionic bonds between amine species and sulfonated groups. Two linkers without and with sulfonated groups are applied to fabricate the semi-IPNs. The core properties of the membranes, like phase separation, water uptake, proton conductivity and methanol permeability, are systematically studied and compared. The DMFCs assembled by using the semi-IPN membranes display better performance than Nafion 117 in high concentration methanol solutions. The present work provides a facile way to prepare PEMs with enhanced DMFC performance.