It is crucial to clarify the permeation behavior of O2 through the ionomer film for enhancing local O2 transport in cathodes of fuel cells. However, all existing studies mainly deal with pure O2 rather than air. Herein, the permeation behavior of the O2/N2 mixture through the ionomer film has been well explored in view of molecular bond length variations by molecular dynamics simulations. The bond lengths for O2 and N2 are shortened under a low hydration level when permeating through a dense layer with small free voids while no obvious change occurs at higher hydration. In the bulk ionomer region, O2 molecules residing in water domains are energetically unstable because the bond lengths deviate far from the equilibrium length; thus, O2 diffuses through the interfacial or hydrophobic regions. N2 molecules show similar properties with O2. This study provides a novel perspective on the permeation behavior of O2 and N2 through the ionomer film, which definitely benefits enhancing local O2 transport.