Novel Nafion/Hydroxyapatite (HA) composite membrane with high crystallinity was fabricated to suppress methanol crossover for direct methanol fuel cell (DMFC) applications. In this study, water and methanol diffusivity were evaluated through water-methanol sorption/desorption test and methanol permeation experiments. It was shown that the water-methanol diffusivity and methanol crossover for the composite membranes decrease as HA increases. Structural variation was investigated with wide-angle x-ray. As a result, it was found that the crystallinity of composite membranes increases with HA whereas water uptake content decreases gradually. Methanol permeability using a diffusion cell reduced in the composite membranes, suggesting that high crystallinity and low water uptake of composite membrane result in the suppression of methanol crossover due to the incorporation of HA into Nafion structure.