Chitosan biopolymer has been extensively applied in direct methanol fuel cells (DMFCs) as a potential replacement to conventional Nafion membrane for its considerably reduced methanol crossover. Here, we computationally explored the influences of methanol concentration, temperature, and pH parameters upon the nanostructure and dynamics, particularly the methanol crossover, in chitosan proton-exchange membrane (PEM) through molecular dynamics simulations. Theoretical results demonstrated the increased swelling and radius of gyration of chitosan chains at higher concentrations. Structural examinations further revealed that an increase in methanol loading weakened the water interactions with chitosan functionalities (amineNH , hydroxylOH, and methoxyCH OH) whereas improved the methanol affinities toward chitosan, reflecting higher methanol sorption capability of chitosan at enhanced concentrations. Additionally, it was found that interactions between solvents and chitosan strengthened under acidic pH conditions on account of amine protonation. The water diffusivity inside the swollen chitosan diminished by increasing CH OH uptake, and in contrast diffusivity of methanol was noted to enhance. Furthermore, it was observed that an enhancement in temperature or a decrease in pH intensified solvent mobility. These insights imply that supplying methanol-concentrated and/or acidic feed solutions into DMFCs based on chitosan PEMs could lower membrane performance due to the significant methanol transport dynamics.