Proton exchange membrane fuel cells (PEMFC) have wide application prospects. In order to improve the comprehensive performance of PEMFC with flow channel configuration, a single-phase, three-dimensional, isothermal model of PEMFC with circular staggered labyrinth flow channels was established, and the effects of new flow channels on the output performance, cathode oxygen and water concentration distribution and cathode inlet flow rate of PEMFC were analyzed. The results show that the current density of circular staggered channel is increased by 25% and 143% compared with rectangular staggered channel and serpentine channel, the distribution and transportation of reactants and products in the channel can also be obviously improved. The increase of cathode inlet flow rate can improve the performance of the PEMFC, but it will also bring other additional losses. It is concluded that the circular staggered flow channel can effectively improve the output performance of PEMFC and improve the distribution of oxygen and water.