Recently, the applications of non-equilibrium plasma in atmospheric pressure to medical treatment have been developed on the basis of stabilization techniques of the plasma formation. However, the biological response by the plasma is not well understood because of the complicated reaction processes. In the present work, the reactive interaction between active oxygen and phospholipid was simulated with quantum mechanical molecular dynamics in order to investigate the mechanism of response by plasma irradiation on biomembrane. The difference of reaction processes in phosphatidylcholine was shown against the irradiation energy and direction of oxygen atom. The time evolution of energy in the present molecular system was appropriated at very low and room temperatures in comparison with similar reaction processes between oxygen radical and ethane.