The optimal design of variable section is a flow field optimization method that changes the pressure of the reacting gas in the flow channel by setting up a contraction surface in the flow channel, which is effective in improving many aspects of the proton exchange membrane fuel cell (PEMFC) performance. However, there are also problems such as uneven oxygen distribution in some of the flow channels, and the current density and net output power are not significantly improved. To find a balance among gas transfer efficiency, drainage capacity, uniformity of current density distribution, and output performance, this paper investigates the design of a variable cross-section-enhanced mass transfer flow field for PEMFC flow channel contraction by establishing a three-dimensional numerical model, starting from the sidewall width direction and the bottom height direction of the flow channel cross-section dimensions, in order to assess the effects of variable cross-section contraction at the bottom and sidewalls of the flow channel on the cell performance. The polarization curves, mass transfer capacity, current density distribution, and net output power of the variable cross-section contraction flow field are analyzed and compared with the straight flow field. On this basis, the optimum size parameters and operating parameter combinations are determined. Variable cross-sectional contraction flow field improves PEMFC output performance. The contraction of the variable cross-section contraction flow field at the sidewalls effectively improves reactive gas transfer efficiency and drainage capacity, improves current density distribution, and increases the net output power of the PEMFC. In particular, the sidewall contraction flow field has a 9.0% increase in power density, a 6.45% increase in the effective mass transfer coefficient (EMTC), a 6.52% increase in uniformity of current density distribution, and a 6.05% net power increment compared to the straight flow field, respectively. The best output performance, the highest oxygen concentration, and the lowest water concentration are achieved with a combination of parameters: number of sidewall contractions N = 6 , length L f = 6 mm , and width W f = 1.2 mm . And a wide range of air stoichiometry ratios are applied when the contraction of the variable cross-section contraction flow field is located at the sidewalls. Increasing the cathode stoichiometry ratio from 10 to 50 increased the cell power density by 25.5% and from 50 to 90 increased the cell power density by 9.5%. The simulation results can provide theoretical basis for the application of variable section flow field design for practical PEMFC.