Proton exchange membrane fuel cells (PEMFC), which convert the chemical energy into electrical energy directly through electrochemical reactions, are widely considered as one of the best power sources for new energy vehicles (NEV). Some of the major advantages of a PEMFC include high power density, high energy conversion efficiency, minimum pollution, low noise, fast startup and low operating temperature. The Membrane Electrode Assembly (MEA) is one of the core components of fuel cells, which composes catalyst layers (CL) coated proton exchange membrane (PEM) and gas diffusion layers (GDL). The performance of MEA is closely related to mass transportation and the rate of electrochemical reaction. The MEA plays a key role not only in the performance of the PEMFCs, but also for the reducing the cost of the fuel cells, as well as accelerating the commercial applications. Commercialized large-size MEA directly plays a major role in determining fuel cell stack and vehicle performance. In this work, commercial sample A and B from two different batches of the MEA production line are tested. Compared with the polarization curve, the current density of type A and type B MEA are 1.84 A·cm-2 and 1.28 A·cm-2 respectively. In terms of current density, the result of type A is 43% higher than the one of type B. In addition, the morphology and electrochemical test are used to explain the reasons for the different performance between type A and type B. According to the result, it can be seen that the electrochemical properties of the catalyst in type A is superior than type B. Meanwhile, the pore size and blow-hole rate of the GDL in type A is larger than that in type B. Thus, the performance of type A is better than that of type B.