The overpotential at the cathode is significantly large in the proton exchange membrane fuel cells; therefore, the oxygen concentration in the oxygen reduction reaction (ORR) area is vital. Condensed water in the flow field and the gas diffusion layer (GDL) reduces oxygen transport to the ORR area. The enhancement of the mass transport of liquid water and oxygen is critical to improve fuel cell performance particularly at the high current density operations. It is required to reduce the total active area in the fuel cell stack and also it is leading to the significant cost reduction. Experimental investigation of oxygen transport has been limited by an inability to resolve water saturation-dependent properties. The two-phase thermos-fluid dynamics model of GDL was developed with Lattice Boltzmann Method (LBM) and it was integrated with computational fluid dynamics (CFD) based proton exchange membrane fuel cell (PEMFC) model to simulate the fuel cell performance with given design parameters and operational conditions [1, 2]. This work, utilizing the developed model, investigates the correlations between fuel cell performance and GDL structures and material properties. Some empirical studies were pursued and structure and property of the micro porous layer (MPL) in the GDL is correlated to the fuel cell performance particularly high current densities [3-5]. The model simulates the fuel cell performance with various porosity and permeability of MPL in the cathode GDL to investigate those correlations. Also the two-phase model can show the presence of residual liquid water in the cathode GDL which effects on the fuel cell performance. It can distinguish the residual liquid water in the GLD underneath of the flow field channel ribs and under the channels. Figure 1 gives an concept of integrated CFD based PEMFC model with micro-scale GDL model with LBM. Figure 2 shows residual liquid water in the cathode GDL with various operating conditions. In this fuel cell design, residual liquid water is correlated with cathode conditions, relative humidity, rather than the current density. It shows the potential capability of a model-based investigation of mass-transport to find solution of design and operational conditions in the PEMFC.