The ion exchange membrane is one of the key components of membrane-electrode assembly (MEA) at PEMFC and AEMFC systems, which plays important role in fuel cell performance together with catalysts. It is widely accepted that water channel morphology inside ion exchange membranes as ions pathway significantly affects the ion exchange membrane performance. So, molecular dynamics (MD) simulations are a very useful tool to understand molecular and atomic structures of materials, so that many related researches are currently being studied. In this paper, we summarize the current research trend in MD simulations, present which properties can be characterized, and finally introduce the usefulness of MD simulations to the researchers for ion exchange membranes.