The biological reduction of N2 to NH3 catalyzed by molybdenum nitrogenase requires eight steps to finish a completed catalysis cycle. This reaction cycle is associated with ATP-driven electron transfer (ET) from the Fe protein to the MoFe protein, and part of ET is experimentally confirmed to be ‘conformationally gated’. Although the overall sequence of ET in nitrogenase has been studied for decades, the nature of coupling between ET pathways and nucleotides binding/protein-protein docking is still unclear, especially from theoretical aspects. Here, we have utilized submicrosecond classical molecular dynamics simulations to allow the ADP-bound and ATP-bound nitrogenases to simulate their conformations in real biological systems. Then the Pathways plugin implemented by Balabin et al was employed to calculate the ET coupling and visualize the ET pathways between the F-cluster and the P-cluster in nitrogenase. The comparison of the ET couplings (the F-cluster to the P-cluster) we calculated and the edge-to-edge distance between the ET donor and acceptor suggests that the coupling pathways grow in strength more that that would be expected from simple distance changes. This result additionally indicates the electron of Fe protein is protected prior to the ATP binding and the protein-protein docking, using pathway switching effects.