The air supply system has a significant effect on the efficiency of polymer electrolyte membrane fuel cell (PEMFC) systems. The performance and efficiency of automotive PEMFC systems are greatly influenced by their air supply system configurations. This study deals with the system simulation of automotive PEMFC systems using MATLAB/Simulink framework. In this study, a low-pressure operating PEMFC system adopting blower sub-module (turbo-blower) is modeled to investigate the effects of stack operating temperature and air stoichiometry on the parasitic power and efficiency of automotive PEMFC systems. In addition, the PEMFC net system efficiency and parasitic power of air supply system are mainly compared for the two types (low-pressure operating and high-pressure operating) of automotive PEMFC systems under the same net power conditions. It is suggested that the obtained results from this system approach can be applied for establishing the novel operating strategies for FC vehicles.