This study combined the experimental and modeling methods to investigate effects of different factors on the performance of the micro-PEM fuel cell (μ-PEMFC). The results showed that species transport and contact resistance determined the performance of the μ-PEMFC. Contact resistance in the μ-PEMFC contributed to 19.4% of the total inner resistance in this study. The contact resistance changed significantly the distribution of overpotential in the μ-PEMFC and decreased the current output. Small dimensions of the μ-channel drastically affected the species transport and resulted in a non-uniform current distribution along channel direction at low cell potential (high current). Therefore, the designs of new flow field configurations and assembling modes of μ-PEMFCs are very important in improving the performance of μ-PEMFCs. These designs including flow field and assembling mode of μ-PEMFCs should improve species transport through μ-channels and decrease the contact resistance between gas diffusion layers (GDLs) and current collectors.