Summary Gas diffusion layer (GDL) plays an important role in the performance of membrane electrode assembly (MEA) in polymer electrolyte fuel cells. In this work, 2‐type MEAs were prepared by 2 different GDLs of 29 BC and 29‐WUT, and the performance were investigated using polarization curve methods. The performance of MEA with 29‐WUT was 120 mV higher than 29 BC at 1600 mA/cm2. Electrochemical impedance spectroscopy (EIS) was applied to measure the mass transport resistance of 2‐type MEAs under normal running condition. The results of EIS showed that the mass transport resistance of 29 BC was 3.15 times higher than that of 29‐WUT at 1600 mA/cm2. To clarify this phenomenon, limiting current methods were applied under diluting oxygen concentration, low humidity, and high flow rate conditions. The results of limiting current methods showed that both the total oxygen transport resistance and the molecular diffusion resistance in the GDL of 29 BC were larger than that of 29‐WUT due to the lower porosity of gas diffusion substrate in 29 BC. As a result, EIS can be well combined with limiting current methods to analyze oxygen transport resistance in GDLs of fuel cells.