In this study, a three-dimensional numerical model of an ejector is established, which is based on a 40 W power proton exchange membrane fuel cell (PEMFC) system. Computational Fluid Dynamics (CFD) technique is used to analyze the ejector in low power condition. The effects of two key structural parameters (distance from the mixing chamber to the nozzle and the mixing chamber diameter) on the ejector performance at different currents are investigated. It is found that ejector entrainment ratio changes slightly with the distance from mixing chamber to nozzle. The ejector entrainment ratio increases first and then decreases with the mixing chamber diameter. Moreover, with the increase of mixing chamber diameter, the turbulent kinetic energy and turbulent dissipation rate decrease obviously.