Hydrogen has the potential to serve as a new energy resource, reducing greenhouse gas emissions that contribute to climate change. Natural hydrogenases exhibit impressive catalytic abilities for hydrogen production, but they often lack oxygen tolerance. Oxygen-tolerant hydrogenases can work under oxygen by reacting with oxygen to form inactive states, which can be reactivated to catalytic states by oxygen atom removal. Herein, we synthesized three NiFeSe complexes: (NiSe(CH3)FeCp, NiSe(CH3)FeCp* and NiSe(PhNMe2)FeCp) with features of active sites of [NiFeSe]-H2ases, which are the oxygen-tolerant hydrogenases, and we investigated the influence of electronic and steric factors on the oxygen reaction of these “biomimetic” complexes. In our research, we found that they react with oxygen, forming 1-oxygen species, which is related to the O2-damaged [NiFeSe] active site. Through a comparative analysis of oxygen reactions, we have discovered that electronic factors and steric hindrance on Se play a significant role in determining the oxygen reactivity of NiFe complexes related to hydrogenases’ active sites.