Understanding molecular interactions between oil and reservoir matrix is crucial to develop a productive strategy for enhanced oil recovery. Molecular dynamics simulation has become an important method for analyzing microscopic mechanisms of some static properties and dynamic processes. However, molecular modeling of shale oil and reservoir matrix is still challenging, due to their complex features. Wettability, which is the measurement of oil-matrix interactions, requires in-depth understanding from the microscopic perspective. In this study, the density, interfacial tension and viscosity of eleven common components in shale oil are calculated using molecular dynamics simulations. Then a molecular model of Gulong shale oil is built, based on the reported experimental results and simulations. Compared with the variation in hydrocarbon content, the change in polar component content leads to more significant variations in the physical properties of shale oil. This molecular model is also employed to investigate the wettability of shale-oil nanodroplets on minerals and organic matter, with or without the surrounding aqueous phase. This work suggests fresh ideas for studying the oil-matrix interactions on the nanoscale and provides theoretical guidance for shale oil exploitation.