The value of crude oil accommodated in shale has been recognized and has attracted increasing attention from the academic and industrial society. The occurrence and mobility of crude oil in clay pores, therefore, become essential issues for evaluation and recovery of shale oil. The distribution, structure, and transport of the oil-brine mixture confined in a slit-shaped montmorillonite mesopore with different water amounts have been investigated using equilibrium molecular dynamics and nonequilibrium molecular dynamics (NEMD) simulations. A mimic model of crude oil, a mixture of 19 organic molecules, was employed, and thus the behavior of different organic molecules could be characterized in detail. A temperature of 410 K and a pressure of 300 atm corresponding to a buried depth of 3 km were employed. The simulations indicate that the water the distribution of crude oil. Water and metal ions prefer to cover on hydrophilic montmorillonite surfaces, while nonpolar hydrocarbons tend to be far away from clay surfaces. As the water amount is too low to completely cover the clay surfaces, some polar organic molecules will come into contact with the uncovered clay surface. Abundant organic acid molecules adsorb onto montmorillonite surfaces mainly through participating in the inner-sphere complexes of Na+ ions closely located at montmorillonite surfaces (i.e., Na+ cation bridge) and forming hydrogen bonds with water molecules in the vicinity. Carbazole molecules tend to aggregate together due to pi-pi stacking, while thioether molecules mix within alkane molecules and exhibit no characteristic distributions. The mobility of all oil components decreases with the decrease of the water amount, and the mobility of polar components (i.e., organic acid and carbazole) is relatively lower than that of nonpolar hydrocarbons. NEMD simulations clearly indicate that the transport velocity of crude oil markedly increases with the water amount under a specific pressure gradient. The brine covering on clay surfaces significantly weakens oil-clay interfacial interactions. Polar components, especially organic acid, exhibit relatively low transport velocity compared with nonpolar hydrocarbons. These findings highlight the understanding of physical-chemical behaviors of shale oil and provide atomistic information for technology development for enhancing oil recovery.