Abstract: The global energy demand is increasing rapidly, and it is imperative to develop shale hydrocarbon resources vigorously. The prerequisite for enhancing the exploitation efficiency of shale reservoirs is the systematic elucidation of the occurrence characteristics, flow behavior, and enhanced oil recovery (EOR) mechanisms of shale oil within commonly developed nanopores. Molecular dynamics (MD) technique can simulate the occurrence, flow, and extraction processes of shale oil at the nanoscale, and then quantitatively characterize various fluid properties, flow characteristics, and action mechanisms under different reservoir conditions by calculating and analyzing a series of MD parameters. However, the existing review on the application of MD simulation in shale oil reservoirs is not systematic enough and lacks a summary of technical challenges and solutions. Therefore, recent MD studies on shale oil reservoirs were summarized and analyzed. Firstly, the applicability of force fields and ensembles of MD in shale reservoirs with different reservoir conditions and fluid properties was discussed. Subsequently, the calculation methods and application examples of MD parameters characterizing various properties of fluids at the microscale were summarized. Then, the application of MD simulation in the study of shale oil occurrence characteristics, flow behavior, and EOR mechanisms was reviewed, along with the elucidation of corresponding micro-mechanisms. Moreover, influencing factors of pore structure, wall properties, reservoir conditions, fluid components, injection/production parameters, formation water, and inorganic salt ions were analyzed, and some new conclusions were obtained. Finally, the main challenges associated with the application of MD simulations to shale oil reservoirs were discussed, and reasonable prospects for future MD research directions were proposed. The purpose of this review is to provide theoretical basis and methodological support for applying MD simulation to study shale oil reservoirs.