This paper reports the negative effect of the cracked gas diffusion layer (GDL) on the performance of polymer electrolyte membrane fuel cells (PEMFCs) under varying flow channel width. The polarization characteristics and the corresponding electrochemical impedance spectra of the PEMFCs with pristine GDLs and cracked GDLs were computed. The results showed that for PEMFCs with 1.0 mm flow channels, the power density rates of reduction between the PEMFCs with pristine GDLs and those with cracked GDLs were 2.8% under the condition of oxygen and 6.6% under the condition of air. On the other hand, for the PEMFCs with 0.5 mm flow channels, these values were 10.3% under the oxygen condition and 14.2% under the air condition. This implies that the thinner the flow channels, the more severely the cracked GDLs influence the PEMFC performance in terms of concentration loss. The EIS data indicated that, compared to the PEMFCs with 1.0 mm flow channels, the cracks on GDLs had more impact on the PEMFCs with 0.5 mm flow channels with regard to activation overvoltage.