The spatial distribution of Li ions in electrochemically lithiated graphite anodes for Li-ion battery is characterized by scanning Auger electron microscopy. We show that direct mapping of Li KVV peak intensity reveal the spatial distribution of intercalated Li and its chemical state in a quantitative manner. Furthermore, we demonstrate that mapping using a C KVV peak also reflects the spatial distribution of Li due to the change in the electronic properties of C atoms induced by the electrode reaction (Li intercalation). Mapping measurements on three samples with different charging states (20%, 50%, and 100%) show that at the early stage of charging Li ions do not intercalate homogenously into all the graphite particles but selectively into some specific ones with higher rates. Our method provides the criteria to evaluate structure-correlated Li intercalation from nanometer- to micrometer-scale, such as conductivity network in the electrodes due to a non-uniform morphology of binder and conductive additives.