Cathode catalyst layer plays an important role in PEMFC. Electrochemical reaction in cathode catalyst layer is a control process for the performance in PEMFC. In this paper, oxygen reduction reaction (ORR) is studied by molecular simulations based on a series pathway which consist of four steps. We calculated the free energy of four steps respectively by molecular simulations. Comparing free energy of our steps, we found that the fourth step can release more energy than the other steps. At the same time, we found that the energy released in ORR is decreased with the increase of temperature. The process of the first step in the series pathway release less energy than that of other steps. The results are very helpful for optimization of construction in the cathode and improving performance of PEM fuel cell.