The effects of water cluster structures on proton transport properties have been studied using reactive molecular dynamics simulations. The proton diffusivity and proton distributions have been evaluated in the two hydrophilic cluster structures (i.e., the cylinder model and the lamellar model) that are the most typical proposed morphological models in polymer electrolyte membranes. The proton transport with the Grotthuss mechanism has been incorporated using the modified two-state empirical valence bond (aTS-EVB) model. The diffusion coefficients in each dimension are correlated with the cluster size as well as the type of cluster models. It is found that the proton diffusion coefficients strongly depend on the cluster model and its size. The proton distributions are also investigated to elucidate the proton pathway in each cluster model. Our simulation results provide insight into quantitative information about the water cluster structure dependence of the proton transport properties at an atomic level.