The molecular structural information on a kerogen isolated from Huadian oil shale was obtained using solid-state 13 C nuclear magnetic resonance (NMR), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR), and X-ray diffraction (XRD) techniques. Then, a series of Huadian kerogen isomers were constructed on the basis of these structural data. The possible carbon skeleton isomer and the substituted position effects of the aromatic ring, aliphatic ether bond, carboxylic acid, and carboxylic acid derivative as well as the quantity of tertiary and quaternary carbons on Huadian kerogen model stability have been systematically studied on the basis of density functional theory (DFT) calculations. For the carbon skeleton isomer, the calculated total energy decreases with the increasing number of the closed annular space (grid), which is constituted by connecting the aliphatic chain to the aromatic cluster or other aliphatic chain. DFT calculations show an about 16.8 kcal mol −1 decrease in total energy for every grid increase when the number of grids increases from 2 to 11. A significant break in the decrease of the total energy has been obtained for an isomer with 11 grids, which means that a proper number of grids (11 grids is appropriate in this paper) in carbon skeleton should be considered for building the chemical structure of Huadian kerogen. For the substituted position effects, aliphatic ether bonding to quaternary carbon, carboxylic acid attaching to secondary carbon, and carboxylic acid derivative bonding to quaternary carbon seem to give a lower energy structure than other connections. Besides, a high quantity of tertiary and quaternary carbons is conducive to a stable model for Huadian kerogen. The aromatic cluster dispersed distribution also makes a contribution to improve the stability of the model. According to these results, we proposed a relatively stable Huadian kerogen three-dimensional (3D) model. Moreover, this 3D model was testified reasonablely through the match between calculated and experimental 13 C NMR spectra.