The dynamic structural change of graphite during the electrochemical lithium intercalation at 1/3C was identified by an in situ high energy synchrotron XRD. Thanks to the fast data collecting detector and high energy X-ray beam of this characterization technique, the detailed structure change of graphite was monitored. Under a high current density, the voltage plateaus in discharge curve and superlattice peaks in XRD patterns were not observed. These results indicated that the dynamic lithium intercalation behavior was remarkably different from that described by the classical staging mechanism. Instead, a Li-riched phase as well as a series of intermediate phases for the x value in Li x C6 being larger than 0.5 were identified. This dynamic phenomenon was considered to be synergistically affected by the driving force of the intercalation reaction, van der Waals force between graphene layers and repulsive interaction between the intercalated Li specie. Basing on the experimental results, a dynamic mechanism was proposed.