In this paper, the flow channel of the radial proton exchange membrane fuel cell (PEMFC) is optimized by the topological optimization method. Using the SNOPT algorithm, a two-dimensional stable constant temperature model is freely constructed in the cyclic sector design domain. Topology optimization aims to maximize the efficiency of PEMFC and minimize the energy dissipation of reaction gas. We analyze radial topology flow channels’ mass transfer capacity and cell performance with different maximum volume constraints. The results show that under high current density, the performance of the optimized channel is significantly better than that of the traditional channel. Increasing the maximum volume constraint is beneficial for improving the mass transfer of PEMFC. At 0.6 V, the cell performance of Scheme 4 is 14.9% higher than the serpentine flow channel and 9.5% higher than the parallel flow channel. In addition, in the optimal selection, 3D simulation modeling is carried out for more accurate verification.