This paper proposes a hierarchical model for automotive fuel cell system evaluation, comparison and applicability assessment through Analytic Hierarchy Process. A dual-layer criterion based hierarchical model is proposed, which features 9 sub-performances and 18 indices. Criterion weights and scoring function are both established. Experimental application is carried out to illustrate the evaluation process and how the proposed model operates. Results show that the sub-performance derived from automotive powertrain requirements represented the overall characteristics of the PEMFCs. The selected 18 most significant indices also made each sub-performance quantitatively assessable. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.