The cathode flow channel of proton exchange membrane fuel cell (PEMFC) serves as the site of oxidant reduction, and the interaction of the flow channel configuration and operating parameters is one of the keys to enhance the performance of the cell. A three-dimensional proton exchange membrane cell model with cathode sidewall shrinkage runner was established to meet the design requirements of PEMFC sidewall shrinkage runner regarding the operating parameters. The changing rules of electrochemical performance, temperature distribution on the membrane surface and water content distribution were investigated under different temperatures, pressures and cathode stoichiometric ratios. It is shown that under the constant operating parameters, the current density curves of the ridge centerline and the flow channel centerline are impulsively fluctuated, and the temperature curves of the membrane surface and the water content curves of the membrane surface are regularly fluctuated. The current density, temperature and water content at the ridge centerline are obviously higher than those at the flow channel centerline. Under the change of operating parameters, when the pressure is increased from 0.1 MPa to 0.3 MPa, the current density is increased from 0.860 A/cm² to 1.500 A/cm², with an increase of 74.4%. When the temperature is increased from 50 ℃ to 80 ℃, the current density is increased from 0.822 A/cm² to 0.856 A/cm², with an increase of 4.1%. And when the cathode stoichiometry ratio is increased from 10 to 90, the current density is increased from 1.502 A/cm² to 1.568 A/cm², with an increase of 4.4%. Furthermore, a PEMFC output performance evaluation method based on the combined assignment method and the improved radar diagram method has been established. The cathode sidewall-retracted proton exchange membrane fuel cell is shown to exhibit excellent output performance under the operating parameters of 0.25~0.3 MPa, 70~80 ℃ and the stoichiometric ratio in the range of 70~90.