| Summary: | The understanding of the relationship between the chemical structure and the hydrophilic structure is crucial for the designing of high-performance PEMs. Comparative studies in typical Nafion and sulfonated poly (ether ether ketone) (SPEEK) were performed using a combined experimental and theoretical method. SPEEK showed suppressed fuel crossover and good mechanical property but low water uptake, weak phase separation, and inadequate proton conductivity. Molecular dynamics (MD) simulation approaches were employed to get a molecular-level understanding of the structure−property relationship of SPEEK and Nafion membranes. In SPEEK membranes, the local aggregation of hydrophilic clusters is worse, and much stronger electrostatic interaction between O<sub>s</sub>−H<sub>h</sub> was verified, resulting in less delocalized free H<sub>3</sub>O<sup>+</sup> and much lower D<sub>H3O+</sub>. In addition, the probability of H<sub>2</sub>O−H<sub>3</sub>O<sup>+</sup> association varied with water content. Particularly, SPEEK exhibited much lower H<sub>9</sub>O<sub>4</sub><sup>+</sup> probability at various relative water contents, leading to lower structural diffusivity than Nafion. Eventually, SPEEK possessed low vehicular and structural diffusivities, which resulted in a low proton conductivity. The results indicated that the structure of hydrated hydronium complexes would deform to adapt the confining hydrophilic channels. The confinement effect on diffusion of H<sub>2</sub>O and H<sub>3</sub>O<sup>+</sup> is influenced by the water content and the hydrophilic morphologies. This study provided a new insight into the exploration of high-performance membranes in fuel cell.
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