Chitosan materials were constructed to study the ion conductivity mechanism of chitosan membrane at the molecular level. The proposed systems represented the PEM fuel cell composed of chitosan, hydronium ions and 10 or 40% wt of water. The molecular dynamics simulation was used to estimate the different coefficient, the ion conductivity, and the coordinations between particles. System of water 40% water by weight can act as a conducting materials, which gives conductivity as high as 7.14× 10⁻²S/cm. The results were compared to the reference experimental data. The coordination was also studies to evaluate the location of particles in system to understand the transport mechanism of the ions. As a result, eigen ion (H₉O₄+ ) and water cluster play a major role in obtaining the conductivity.