The flow field design of the proton exchange membrane fuel cell (PEMFC) had a great impact on the performance and lifespan of the cell. To improve the uniformity of the substance component inside the PEMFC, referring to the serpentine flow field, a kind of compensating flow field is designed and investigated. Under the same conditions, the homogeneity of the two flow field structures is compared, and the influence of the homogeneity of two flow field distributions on the performance of the PEMFC is further analyzed. The polarization curve, maximum pressure difference at the inlet and outlet of the flow channel, and thermal stress generated by temperature gradients are used as performance indicators for evaluating the performance of the cell. The results show that after compensation, the distribution uniformity of each component in the flow field is improved, and the power density, water management, and thermal management capabilities are better than those in the traditional flow field design. Furthermore, the thermal performance of the single-layer cell and five-layer stack was compared. The results show that the more fuel cell layers, the greater the temperature difference within the cell, which will result in greater thermal stress. In the compensation flow field, the thermal stress of a single-layer unit is 14% lower than that of a serpentine flow field, and the thermal stress of a five-layer stack is 20% lower.