Accurate kinetic models are of great significance for the simulation and analysis for hydrogen fuel cells. The proton exchange membrane (PEM) fuel cell is a complex nonlinear, multi-variable system. The mathematical modeling of PEM fuel cell usually leads to nonlinear parameter estimation problems which often contain more than one minimum. In this paper, a novel bio-inspired P systems based optimization algorithm, named BIPOA, is proposed to solve PEM fuel cell model parameter estimation problems. In BIPOA, the nested membrane structure and new rules such as adaptive mutation rule, partial migration rule and autophagy rule are combined to improve the algorithm's global search capacities and convergence accuracy. Studies on some benchmark test functions indicate that the BIPOA outperforms the other two methods (PSOPS and GAs) in both convergence speed and accuracy. In addition, experimental results reveal that the model predictive outputs are in better agreement with the actual experimental data. Therefore, the BIPOA is a helpful and reliable technique for estimating the PEM fuel cell model parameters and is available to other complex parameter estimation problems of fuel cell models. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.