In this study, we report the effects of Nafion thickness on the performance of ionic polymer-metal composite (IPMC) actuators. We analyzed the actuation properties of the IPMC actuators, such as displacement and tip force, under external voltage, as a function of their thickness. In order to understand the relationship between thickness and actuation properties, we developed a semi-quantitative model of voltage induced ionic diffusion and its contribution to bending of the Nafion cantilever. Furthermore, we investigated the mechanical properties of the Nafion membranes at sub-micro scale as well as bulk scale, using atomic force microscopy (AFM) and tensile test. The results of the two methods indicated opposite trends of elastic modulus and crystallinity as a function of thickness. We hypothesized that the hot-pressed Nafion was composed of three layers with different crystallinity. Our results suggest that for a high performance IPMC actuator, we need better control of the annealing temperature gradient.