The delithiation reaction in lithium ion batteries is often accompanied by an electrochemically driven phase transformation process. Tracking the phase transformation process at nanoscale resolution during battery operation provides invaluable information for tailoring the kinetic barrier to optimize the physical and electrochemical properties of battery materials. Here, using hard X-ray microscopy--which offers nanoscale resolution and deep penetration of the material, and takes advantage of the elemental and chemical sensitivity--we develop an in operando approach to track the dynamic phase transformation process in olivine-type lithium iron phosphate at two size scales: a multiple-particle scale to reveal a rate-dependent intercalation pathway through the entire electrode and a single-particle scale to disclose the intraparticle two-phase coexistence mechanism. These findings uncover the underlying two-phase mechanism on the intraparticle scale and the inhomogeneous charge distribution on the multiple-particle scale. This in operando approach opens up unique opportunities for advancing high-performance energy materials.