Electrochemical impedance spectroscopy (EIS) is a widely used technique to measure the properties of materials in electrochemical systems. However, the obtained quantities are difficult to directly connect to the microstructure-level phenomena. In this work, detailed electrochemical microstructure simulations were performed to investigate the EIS behavior of the phase-separating graphite electrodes. The Cahn–Hilliard phase-field equation was employed to model Li transport in the graphite particles. In graphite electrodes that were in single-phase stages, the obtained charge-transfer resistance reflected the total active surface areas. The effect of pore tortuosity, which dominates an electrode’s high-rate performance, cannot be reflected in the EIS behavior. In two-phase coexistence graphite electrodes, when phase boundaries were present on the particle surfaces, the simulations exhibited an inductive loop on the simulated EIS curve. In the core–shell phase-morphology cases, the EIS measurements reflected only the properties of the shells. The resulting EIS curves are indistinguishable from those in the single-phase cases. While Fick’s law of diffusion has been mistakenly employed to model Li transport in phase-separating graphite electrodes, our simulations showed that the EIS curves obtained using the Fickian diffusion model are very similar to those obtained using the Cahn–Hilliard phase-field model. This presented tool provides unprecedented detailed simulations to connect the intrinsic material properties, the electrochemical processes in the microstructures, and the resulting EIS behavior.