Nafion nanocomposite membranes with spheric silica, layered silicate (montmorillonite; MMT), and an amphiphilic organic molecule (10-camphorsulfonic acid; CSA) have been investigated as polyelectrolytes for ionic polymer-metal composite (IPMC) actuators. An organosilane (3-mercaptopropyltrimethoxy silane; 3-MPTMS) was grafted on the surfaces of silica and MMT, and the thiol groups on the fillers were sulfonated to endow them with additional hopping sites. The incorporation and modification of the fillers in the Nafion matrix greatly altered the internal morphologies of hydrophilic ion-rich and hydrophobic fluorocarbon regions, followed by changes in mechanical properties, dimensional stabilities, and mass transport kinetics. Finally, the Nafion nanocomposite membranes were engaged as the polyelectrolytes of an IPMC actuator, and actuation performance was analyzed, being associated with the internal morphology-driven diffusion characteristics and capacitances in the polyelectrolyte membranes and the resulting efficiency of charge-to-deformation.