Dynamic variable coupling analysis is an important method to properly design a control structure for complex multivariable and multi-physical dynamic systems, such as fuel cells. The fuel cell is an electrochemical energy conversion device which includes different inter-coupled dynamic phenomena in electrical, fluidic, and thermal domains. In order to achieve optimized fuel cell performance, different operation variables, such as fuel cell temperature, inlet air flow rate, hydrogen pressure, and membrane water content, need to be properly controlled. In this paper, variable coupling analyses of fuel cell dynamic behaviors are presented and discussed based on a proton exchange membrane fuel cell (PEMFC) dynamic model, which considers in particular the transient phenomena in both fluidic and thermal domain. The analyses of dynamic phenomena step responses are conducted using the relative gain array for various control input variables. Quantitative analyses of coupling effects in different physical domains are shown and discussed. The analysis results can be used to optimize the controller design for fuel cell system.