Abstract Water and heat management remains a major obstacle to the successful commercialization of proton exchange membrane fuel cell (PEMFC), especially at a complicated system level. To investigate the interaction among stack and associated auxiliary subsystems, a comprehensive transient PEMFC system model is developed, including stack, membrane humidifier, electrochemical hydrogen pump, air compressor, and radiator. Each individual sub-model has been rigorously validated against experimental data. The results show that the system performance deteriorates significantly under relatively low operating current densities (0.5 A cm−2). The voltage degradation is inhibited as more product water is generated and subsequently utilized by the humidifier, enhancing the stack inlet gas humidification. Under low operating current densities, increasing the operating temperature of membrane humidifier is unfavorable as it exacerbates the membrane dehydration. The voltage undershoot is observed, which is caused by the mismatch between dynamic changes of membrane water content in fuel cell and that of humidifier. If the temperature of dry air flowing into humidifier is well managed, the membrane dehydration may be avoided and assisted heating methods for humidifier may be unnecessary. Increasing the air stoichiometry is disadvantageous as it leads to more generated water being rapidly purged out of the system.