A 3D model for a section of cathode fuel cell comprised of a bipolar plate, a gas diffusion layer (GDL) and a catalyst layer was simulated. The diameter of the carbon fiber GDL is assumed to be the same; moreover, a new and simple method is introduced for the reconstruction of this layer numerically. This method gives the ability to model the heterogeneous and anisotropic structure of the GDL; furthermore, it allows easy implementation and provides realistic results with consideration of the lack of overlap between carbon fibers. The lattice Boltzmann method (LBM) was employed to simulate the flow and the electrochemical reaction. The impacts of changes in the activation potential and the GDL carbon fiber diameter on oxygen species and water vapor, as well as the electric current density distribution over the catalyst layer, were studied. The results showed that at higher values o f the activation potential, the concentration of oxygen near the catalyst layer was lower. The current density over the catalyst layer also increased by increasing the activation potential; on the other hand, the mole fraction of water vapor in the cathode increased with the increase in the flow of gas products. Consequently, results indicated that the variation in the GDL carbon fiber diameter affects the distribution of reactants.