Crystal Orbital Overlap Population (COOP) is one of the effective tools for chemical-bonding analysis, and thus it has been utilized in the materials development and characterization. In this study, we developed a code to perform the COOP-based chemical-bonding analysis based on the wavefunction obtained from a first principles all-electron calculation with numeric atom-centered orbitals. The chemical-bonding analysis using the developed code was demonstrated for F2 and Si. Furthermore, we applied the method to analyze the chemical-bonding changes associated with a Li intercalation in three representative layered materials: graphite, MoS2, and ZrNCl, because of their great industrial importance, particularly for the applications in battery and superconducting materials. The COOP analysis provided some insights for understanding the intercalation mechanism and the stability of the intercalated materials from a chemical-bonding viewpoint.