AbstractLithium iron phosphate (LiFePO4, LFP) serves as a crucial active material in Li‐ion batteries due to its excellent cycle life, safety, eco‐friendliness, and high‐rate performance. Nonetheless, debates persist regarding the atomic‐level mechanisms underlying the electrochemical lithium insertion/extraction process and associated phase transitions. A profound clarity on the fundamental lithium storage mechanisms within LFP is achieved through meticulous scanning transmission electron microscopy (STEM) and selected area electron diffraction (SAED) imaging. This study shows systematical tracking of lithium ions within their respective channels and unveils the phase distribution within individual LFP crystallites not only quantitatively but also at unprecedented atomic‐level resolution. Incontrovertible evidence of the co‐existence of segregated yet only partially lithiated LixFePO4 regions in electrochemically delithiated LFP crystals are provided using correlative electron microscopic methods and data analysis. Remarkably, by directly tracing ion transport within lithium channels a diffusion coefficient range (10−13–10−15 cm2s−1) for correlated lithium ion motion in LFP is estimated and Funke's ion transport jump relaxation model is validated experimentally for the first time. These findings significantly advance the understanding of olivine‐type materials, offering invaluable insights for designing superior battery materials.