Structure transformation and microstructure of the electrode active materials in a graphite / Li （Ni1/3Co1/3Mn1/3）O2 lithium ion battery during charge-discharge process have been studied by XRD. It is found that the lattice parameter of Li （Ni1/3Co1/3Mn1/3）O2, a and c, decrease and increase respectively. Its micro-strain ε and diffraction intensity ratio, I104/I101 and I012/I101, increases and decrease respectively, because Li atoms de-intercalate out of the crystal lattice of LiMO2. Meanwhile, the lattice parameter, a and c, micro-strain ε and stacking disorder P of 2H-graphite all increase, becausing Li atoms to intercalate into 2H-graphite.During charge process, Li atoms occupying （000） sites may preferentially de-intercalate from LiMO2 crystal lattice, and subsequently the Li atoms occupying （2/3 1/3 1/3）and（1/3 2/3 2/3）sites de-intercalate from LiMO2. When intercalating into 2H-graphite, Li atoms preferentially occupy interstitial sites between C atom hexagonal net planes. When the stacking disorder degree reaches a given value, 3R-graphite phase may separate out gradually. When the battery has been fully charged or over charged, LiC12 and LiC6 phases can be formed. During discharge process, intercalation and de-intercalation behaviors of Li atoms are reversed. Li atoms may de-intercalate preferentially from interstitial sites of 2H-graphite and intercalate preferentially into （000） sites of LiMO2 crystal lattice. But these processes are not fully reversible.