In this study, structural parameters of Longkou oil shale kerogen were examined and identified by the combination of pyrolysis-gas chromatography-mass spectrometry, Fourier transform infrared spectroscopy, C-13 nuclear magnetic resonance spectroscopy, and X-ray photoelectron spectroscopy. Based on the experimental data, a three-dimensional kerogen model was generated using quantum chemistry and molecular dynamics methods. The optimized molecular configuration was discussed, which showed good agreement with the experimental results in terms of structural characteristics. Electron density analysis was performed to examine the bonding characteristics of kerogen, and the bond length distribution of the Longkou kerogen model was analyzed, revealing that the S atom exhibits higher affinity for the H atom compared to the aliphatic carbon from the comparison of the electron density of the C-S and S-H bonding regions. Mulliken charge analysis was carried out to evaluate the partial atomic charges of heteroatoms. The charges on the cyclic structure tended to be equally distributed because of the presence of conjugated pi bond, leading to the loss of charges on the N atoms. Besides, the HOMO-LUMO properties of Longkou kerogen were calculated, and a detailed picture of the frontier orbitals of kerogen for the inter- or intramolecular chemical reactions was obtained. This study validated that polycyclic aromatic structures in kerogen play a crucial role in the reactive sites for bond cleavage during the deformation of kerogen.