To explore the mechanism of critical metal (Li+ and Ge4+) occurrence in the organic molecular structures of different rank coals, simulations were investigated using quantum chemical density functional theory. In this paper, Wender lignite, bituminous, and anthracite molecular models were used as organic molecular structures in coal. The electrostatic potential (ESP), frontier molecular orbitals, and Mulliken charges were used to identify adsorption sites in organic molecular structures. Mulliken charge, bond length, Mayer bond order (MBO), and adsorption energy values were used to estimate the binding conformation and strength between organic molecular structures and critical metals (Li+ and Ge4+). The results showed that the negative ESP, the highest occupied molecular orbitals, and negative Mulliken charges in the organic molecular structures were located at the O atom of oxygen functional groups and the aromatic structures, respectively, which were the active sites for critical metal adsorption. Mulliken charge transfer, bond length, MBO, and adsorption energy data suggested that the binding of Li+ with organic molecular structures was controlled by the carbonyl group (C=O), while the aromatic structures had less effect on the occurrence of Li+ in the organic molecular structures. The maximum adsorption energy value for binding Li+ with organic molecular structures was -742.16 kJ/mol. The Ge4+ ions not only showed strong binding ability with oxygen functional groups, but also Ge4+ formed thermodynamically stable half-sandwich complexes with aromatic structures. Therefore, the coal rank had little effect on the binding of Ge4+ with organic molecular structures. Moreover, the binding of Ge4+ with organic molecule structures was enhanced by the synergistic interactions of oxygen functional groups and aromatic structures. The adsorption energy values were up to -8511.43 kJ/mol. The adsorption of organic matter in coal to critical metals (Li+ and Ge4+) generated changes in the spatial configuration of the organic molecular structure, including local twisting of the organic molecular structure in lignite and bending of the aromatic structure in anthracite.