As the preliminary step to elucidate the ion transfer mechanism of lithium (Li) species in the cathode electrode of glassy carbon material, molecular dynamics (MD) simulation was taken place describing the initial thermal movement of two Li atoms in the simulation time range of 10 ps maximally in the hydrogen terminated cluster model, C150H30, at molecular mechanics 2 (MM2) level. The formation of Li2 atom pair is specified in the central area of the cluster model as the result of the structural optimization. In the low temperature range from 4 to 10 K, accompanied by the rotational and stretching vibrational motions, it goes around the central area of the cluster model. Diffusion process of the atom pair is simulated dynamically for the first time in the present study. Decomposition of the atom pair occurred at 50 K and it produces two Li atoms which go and back independently from the center to the edge of the cluster model crossing the CC bonds orthogonally. Formation and diffusion processes of Li2 atom pair may be responsible for the charge–discharge cycles in the glassy carbon electrode in the lithium secondary battery.