Green River oil shale is an organic-inorganic macromolecular composite system. Identifying the interactions between nanoscale organic kerogen and the inorganic mineral matrix in oil shale is an important step towards the design of technologies for economic and efficient recovery of shale oil. Quartz (SiO₂), one of the tectosilicate minerals present in the Green River oil shale, is modeled to determine the interactions with the 3D kerogen model. The molecular dynamics simulation technique is used as the tool for modeling the interactions. Two models with different orientations of quartz mineral and kerogen are built to evaluate the role of mineral orientation on the molecular interactions. The models are simulated at room temperature and pressure (300 K and 1.013 bar). The kerogen-quartz interactions are evaluated with respect to eight kerogen fragments. We observe that different fragments within the 3D Kerogen molecules interact with the quartz depending upon the quartz orientation. In both cases, the unconstrained ammonium (NH₄) ions from the adjacent layer of kerogen migrate to the quartz cavities. All the non-interacting kerogen fragments move away from quartz. The nonbonded interactions between kerogen and quartz are generally electrostatic. The presence of quartz mineral also affects the inter-fragment and inter-layer interactions within the kerogen molecule.