In fuel cells, disparities in individual cell performance can significantly impact various aspects of the overall system, including uneven energy output, accelerated aging, poor system stability, and decreased safety. Hence, enhancing the balance within fuel cells holds paramount importance. Accordingly, this study utilized Matlab and COMSOL to establish a 1D model of the fuel cell stack and a 3D model of individual cells for combined simulation. The aim was to analyze performance discrepancies between individual cells arising from flow distribution issues, investigate how flow rates affect individual cell performance, and ultimately, improve fuel utilization by optimizing individual cell flow channel dimensions. This optimization aimed to address performance deficiencies caused by insufficient gas supply. The research findings indicate that pre-optimization and post-optimization of flow field dimensions, the performance of cells experiencing insufficient gas supply (at the lowest inlet flow rate) improved by 5.59%. Increasing the inlet flow rate enhances individual cell performance, although the degree of performance change gradually decreases with increasing flow rates. Post flow channel optimization, the performance disparity between cells experiencing the maximum and minimum inlet flow rates decreased by 7.7%, consequently improving the overall balance of the stack by 67.3%.