numerically investigated the optimal energy management with the dynamic programing algorithmwhile detailed mass and heat transfer processes inside the PEMFC were not considered. Overall, investigating the water and thermal management with a full-scale PEMFC system which links all associated subsystems with the stack is rarely presented in literature. Establishing a comprehensive PEMFC system is of vital importance for understanding the mutual effects and interaction inside the complicated energy system.In the study, a comprehensive multi-dimensional transient PEMFC system model is developed, integrating the stack sub-model with various auxiliary sub-models such as membrane humidifier, electrochemical hydrogen pump, air compressor, and radiator. To ensure the reliability and accuracy of system model, each individual model is rigorously compared with experimental data. The mutual effects among stack and associated auxiliary subsystems areinvestigated, focusing on the overall water utilization and thermal management. The effects of operating conditions related to stack, membrane humidifier, radiator, and air compressor are studied. The output performance and overall efficiency are compared to give some suggestions on the water and thermal management at an authentic system level.