The electrode structure, especially for the channel depth, plays an important role on the performance of the proton exchange membrane (PEM) fuel cell. In this paper, the performance and electrochemical impedance of the PEM fuel cell are measured experimentally. The simulation results of mass transfer and equivalent circuit for the electrochemical impedance are used to explain the effect of the channel depth on the performance of the PEM fuel cell. These results show that when the cell temperature is lower than the gas humidification temperatures, the performance of PEM fuel cell with the channel depth of 2mm is better than that of 1mm; there is more liquid water saturation in cathode for the channel depth of 1mm than that for the channel depth of 2mm. The charge transfer resistance of the PEM fuel cell with the channel depth of 2mm is less than that with the channel depth of 1mm. These results are very helpful to optimizing structure of the PEM fuel cell.