In this paper, a molecular model based on quantum mechanics and molecular dynamics (MD) is developed to study the transfer mechanisms of proton, phosphoric acid (PA) molecule and dihydrogen phosphate anion (H2PO4-) in PA-doped poly(2,5-benzimidazole) (ab-PBI) membrane. This model couples with intermolecular potential energy, interaction force between two particles, linear momentum conservation equation, angular momentum conservation equation, total energy conservation equation, the radial distribution function and Einstein's law of diffusion. The simulated molecular system consisting of ab-PBI macromolecules doped with PA is optimized to obtain an optimal structure of the amorphous cell unit system. The effects of PA doping level, temperature and electric field intensity on the mass transfer in the ab-PBI membrane are studied. A comparison between this simulation results and experimental data gotten from literatures shows this model and its simulation are reliable. Two kinds of proton transfer mechanisms are evaluated, and the first transfer mechanism, in which H2PO4- takes as a carrier and [-C = N-] takes as a stronghold, is considered as the main proton transfer mechanism in an ab-PBI membrane at the studied doping levels. The diffusion coefficient of PA is about 2.5 times of that of H2PO4-, which indicates the diffusion of H2PO4- controls the mass transfer in the ab-PBI membrane. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.