A three-dimensional (3D) multi-phase numerical model of proton exchange membrane fuel cell (PEMFC) is built. The catalyst layer (CL) spherical agglomerate model is used to replace traditional homogenous model, which can predict the concentration loss in PEMFC more accurately. Utilizing this multi-phase model, the PEMFC with 3D fine mesh flow field is investigated at length, and the liquid water distribution in 3D flow field is qualitatively compared with the experimental image in previous literature. It is found that the 3D fine mesh flow field can improve the reactant gas supply from flow field to porous electrodes significantly and facilitate liquid water removal in PEMFC simultaneously. Therefore, it reduces the concentration loss of PEMFC effectively without increasing the pumping power loss thanks to the greatly increased mass transfer area between gas diffusion layer (GDL) and flow field and vertical flow design of hydrogen and air, which also make the reaction rate distribution in CL more uniform. However, the decreased contact area between GDL and bipolar plate in 3D flow field may decrease PEMFC performance at the current densities where ohmic loss is dominated, but its effect is insignificant.