As one of the most essential components of fuel cells, the commercialized Nafion-based proton exchange membranes(PEMs) suffer from several drawbacks like high cost and methanol permeability. The aim of this work is to fabricate a high performance PEM with combined low cost and methanol permeability together with high proton conductivity. Three-dimensional hierarchical molybdenum disulfide (MoS2) nanoflower is synthesized via a facile one-pot hydrothermal method, and then was embedd into sulfonated poly ether ether ketone (SPEEK) matrix to prepare composite PEM. The three-dimensional hierarchical architectures of MoS2 nanoflower can not only avoid the aggregation of MoS2 nanosheets but also provide abundant surface area and active sites, which are of benefit to fully take advantage of the intrinsic water absorption and methanol diffusion resistance ability of MoS2 nanosheets. The formed hydrogen bond network with water passway contributes to the improvement in proton conduction of composite membrane. As a consequence, composite membrane with 1 wt% MoS2 nanoflower loading content achieves optimized proton conductivity (0.123 S cm(-1), 80 degrees C) and methanol permeability (21.5 x 10(-7) cm(2) s(-1), 70 degrees C), which is 59.7% higher and 79.1% lower than that of SPEEK control membrane. Owing to increased proton conductivity and decreased methanol permeability, the maximum power density of the SPEEK/MoS2-1 composite membrane is 82.7 mW cm(-2) at 70 degrees C, which is nearly 64.7% higher than that of pure SPEEK membrane (only 50.2 mW cm(-2)). Furthermore, the durability test confirms that the SPEEK/MoS2 composite membrane still possesses satisfactory stability even after continuous operation at 70 degrees C for 100 h.