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Abstract Understanding of phase‐stability and nanoscale structural modulation during lithiation of layer materials demand comprehensive analysis of the Li‐containing phases in the solid‐state reaction products. Conventional chemical analysis methods in the transmission electron microscope (TEM) are not ideal to detect Li in partially intercalated nanodomains because Li atoms do not remain stationary under the focused electron beam. An alternate approach combining density functional theory (DFT) modeling and multislice image simulation has been explored in the present study to analyze the intercalated structures and to detect and quantify Li from the recorded high‐resolution TEM (HRTEM) micrographs of partially intercalated phases. HRTEM micrographs from partially lithiated graphite and MoS₂show variations in the interlayer spacings, but are not usually directly interpretable. Hypothetical intercalated microstructures of graphite and MoS₂supercells have been generated using atomic‐scale simulations with systematically varying Li concentrations. The measured interplanar spacings are compared with those of experimentally recorded HRTEM micrographs from lithiated graphite and MoS₂. The results confirm the coexistence of different lithiated phases at localized domains. This understanding of phase transformation and the lithium quantification provides a basis for understanding the structural accommodation of layered materials during intercalation.