The polymer electrolyte membrane (PEM) is one of the principal components for polymer electrolyte fuel cells. In the nanoscopic structure of the membrane, ion clusters are formed by water molecules gathered vicinity of sulfonate groups which are hydrophilic parts of Nafion membrane, and proton transport (PT) are largely attributed to the nanoscopic structure of polymer membranes and water aggregations. Thus, it is critical to understand the PT mechanisms through polymer membrane and clarify an important link between the membrane nanostructure and the PT properties. In the bulk aqueous solution, it is observed that proton mobility is roughly 5 times higher than other cations such as K+ which have an ionic radius similar to the hydronium ions. This property of PT is attributed to a combination of proton hopping, known as the Grotthuss mechanism, and vehicular mechanism where protons diffuse in solution as a hydrated form (e.g. hydronium ions). Many research efforts have been focused on understanding the PT mechanism using theoretical basis for the proton hopping models such as the empirical valence bond (EVB) approaches which allow PT phenomena to be simulated within a molecular dynamics (MD) framework. In PEM, it is considered that proton hopping transport still takes place although the water dynamic property in the bulk aqueous solution is inhibited by a lack of bulk-like water structure due to the phase separation in PEM. Since the phase separation is considered one of the primary factors affecting its performance, the morphological properties of PEM have been studied experimentally and been characterized by proposing the cluster models (e.g., the cylinder model, the lamellar model, and the cluster-rod model) which reasonably fit the experimental scattering spectra. However, a detailed relationship between the morphological features and PT is still under debate. In this study, atomistic MD simulations have been performed to study the effects of water cluster structure on PT properties. The systems were built to closely approximate the proposed hydrophilic cluster structures (the cylinder model and the lamellar model) that are the most major morphological models of Nafion. The PT properties were estimated in terms of diffusion coefficient and proton pathway using a modified EVB model developed based on the previous study of the two-state EVB model by Walbran et al. The diffusion coefficients in each dimension were calculated and correlated with the cluster size as well as the type of cluster models. It was found that proton diffusion is strongly affected by the cluster model and its size, which can be associated with the proton pathway in each cluster model. The influence of the sulfonate groups on the PT properties were also investigated. Our simulation results provide insight into quantitative information about PT properties in atomic level.