Safety remains a major issue for the graphite anode used in lithium-ion batteries. The thermal stability of lithiated graphite was studied by atomic-scale characterization and cell tests. The results revealed that the thermal decomposition of the solid–electrolyte interface is the most easily triggered chemical reaction in lithium-ion cells and plays a critical role in determining the battery safety. It was also shown that natural graphite containing a small amount of 3R graphite had much better thermal stability than mesocarbon microbeads that had no detectable 3R graphite.