Empirical force-field simulations of polymers represent an effective method to obtain structural details, and the relationship between the structure and properties. However, the accuracy of the results depends on the quality of the force field, and generalized force field models are usually not accurate enough for any specific polymers. In this work, an all-atom force field model for perfluorosulfonic acid polymers (PFSA) is firstly developed by use of ab initio calculation, and then optimized based on a set of model organic molecules including perfluoroalkanes, perfluoroethers, and perfluorosulfonic acid. The parameters for bond stretching, bond angle bending and dihedral torsion were primarily derived from ab initio calculations at the B3PW91/6-31G(d, p) level of theory of model organic molecules and ions, while the nonbonded force field parameters were developed in conjunction with molecular dynamics simulation (MD) by computing thermodynamic and structural properties for pure organic liquids. In order to verify the accuracy of our force field model, molecular dynamics simulations were carried out to calculate the spectroscopic and transport properties of NAFION, using our force field model and the literature force field models, respectively. Detailed comparison between the experimental results and simulations proved that our force field model is much superior to the literature models.