Abstract: The molecular modeling of Shenmu coal macerals has been studied and the energy compositions, bond length and bond dissociation energy (BDE) of different types of bonds in the vitrinite and inertinite have been compared by molecular mechanics and semi-empirical calculation method of quantum chemistry. The results show that the torsion energy and van der Waals interaction energy are the main types of energy and the substitution group has a great effect on the total energy of molecular. The aliphatic substitution would lead to the increase of total energy, while the aromatic substitution would lead to the decrease of total energy. The calculated results of bond length show that the bond length of aliphatic C—C is longer than that of aromatic C—C, which indicates that the rupture of aliphatic C—C is easier than that of aromatic C—C on heating. The calculation of BDE shows that the Car—Cal bond has a higher BDE than Cal—Cal, and Car—O bond has a higher BDE than Cal—O bond. And the higher BDE and more aromatic C—C in inertinite structural model than in vitrinite structural model maybe explain the fact that the inertinite has a higher thermal stability than vitrinite.