In this article, multiscale simulation methods were used to study structural and transport properties of Nafion-ionic liquid composite membranes that are novel proton conducting materials for fuel cells. Coarse-grained model for 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) ionic liquid was first developed in the framework of BMW-MARTINI force field. Coarse-grained simulation results of bulk [bmim][BF4] ionic liquid show good agreement with all-atom simulation results and experimental data. Nafion-[bmim][BF4] composite membranes were then simulated using all-atom and coarse-grained models. Ionic liquid cluster formation inside Nafion was revealed by coarse-grained simulations. Diffusion coefficients of both [bmim]+ cations and BF4- anions are reduced by one to two orders of magnitude depending on their concentrations in Nafion membrane. [Bmim]+ cations have faster self-diffusion coefficient than BF4- anions, while this phenomenon is more pronounced when ionic liquids are confined in Nafion. This work provides molecular basis for understanding Nafion-ionic liquid composite membranes. (c) 2013 American Institute of Chemical Engineers AIChE J, 59: 2630-2639, 2013