In this paper, the effect of adding a hydrophobic micro porous layer (MPL) at the cathode side of a PEM fuel cell on the cell performance is investigated. For this purpose, a three dimensional two-phase non-isothermal simulation of cathode side layers of a PEM fuel cell which includes gas channel, gas diffusion layer (GDL), hydrophobic micro porous layer (MPL) and catalyst layer (CL) has been performed. The governing equations of fluid flow in the fuel cell are solved with a multiphase mixture model via developing a code and distribution of velocity, pressure, temperature, species concentration and liquid water saturation at the various layers of the cathode side of fuel cell are obtained. Furthermore, the effect of physical and wetting properties of MPL including thickness, porosity, contact angle and permeability on saturation level and performance of the fuel cell are studied. The results show that by adding an extra micro porous layer between GDL and catalyst layer because of differencing in the wetting properties of the layers, a discontinuity appears in the liquid saturation and species concentration at the contact surface of them. In addition, according to the obtained results, increasing the MPL porosity cause to decreasing liquid water saturation and improving the cell performance. While increasing the MPL thickness decreases the cell performance. In order to validate the results, the performance curves calculated by single and two-phase simulating were compared with experimental results and a good agreement was found between them.