In this study, the chemical structural parameters of a kerogen from Yaojie oil shale were identified and investigated by using experimental data obtained from solid-state C-13 nuclear magnetic resonance spectroscopy, Xray photoelectron spectroscopy, X-ray diffraction, flash pyrolysis-gas chromatography-mass spectrometry, and Fourier transform infrared spectroscopy. Twelve constitutional isomers of the Yaojie 2D models with different grids and their corresponding 3D models were constructed by the combination of molecular simulation methods and multiple testing techniques. Finally, a reasonable 3D model of Yaojie kerogen was determined by a series of anneal dynamics simulations and geometry optimization calculations. From the results obtained by Mulliken population analysis and electron density analysis, the pi-pi conjugation effect among the aromatic ring structures is significantly impacted by the heteroatoms, leading to the accumulation of electrons on heteroatoms. Meanwhile, sulfur, oxygen, and nitrogen in the heterocyclic structures exhibited higher electronic charge density and considerably more reactivity compared with those of other atoms. Moreover, the molecular orbitals of HOMO and LUMO were calculated to examine the properties of chemical reaction of kerogen. The HOMO-LUMO energy gap indicated that the Yaojie kerogen exhibited higher reactivities compared to Type. kerogen.