As pivotal component of hydrogen fuel cell vehicles (HFCVs), proton exchange membrane fuel cells (PEMFCs) play a crucial role in determining performance and energy efficiency of HFCVs. In this study, comprehensive bench tests of fuel cell stack and electrochemical impedance spectroscopy (EIS) tests of single cells were conducted, and influence mechanisms of air intake methods and humidity levels on performance of stack and single cells at different locations were analyzed in depth. The results indicate that counter-flow inlet method exhibits superior voltage output performance and stability across various relative humidity (RH) and current densities (CDs). A moderate increase in RH can mitigate performance degradation, but excessive humidity can lead to flooding. When RH is increased to 60%, the voltage difference between co-flow and counter-flow of fuel cell stack does not exceed 0.05 V at 1.6 A/cm2. Meanwhile, the performance of cells near inlet end plate is consistently worse than those farther away under different inlet conditions. In addition, the performance trend of single cells in serpentine channels aligns with that of fuel cell stack, underscoring strong adaptability of mechanisms influencing performance under different conditions. These findings provide theoretical guidance and data support for optimizing performance and preventing failures in PEMFCs.