Abstract A three-dimensional (3D) numerical model associating the heat/mass transfer and the electrochemical reaction in a proton exchange membrane (PEM) fuel cell is developed in this study, and a miniaturized PEM fuel cell with complex flow channels is simulated. The numerical computation is based on the finite-volume method. Governing equations for flow and heat/mass transfer are coupled with the electrochemical reactions and are solved simultaneously. The latent heat from the condensation of water vapor in cathode channel, if any, is considered. The perimeters of the bipolar plates are also included in the computational domain to account for their heat conduction effect. The miniaturized PEM fuel cell has a membrane electrode assembly (MEA) sandwiched by two brass bipolar plates etched with a number of winding gas channels with a flow area of 250 μm ×250 μm. The influence of anode gas humidity on the performance of the fuel cell is investigated through model prediction. Finally, field details of velocity, mass fraction and electromotive force are illustrated and discussed.