Utilizing CO₂ to enhance shale oil recovery has a huge potential and thus has gained widespread popularity in recent years. However, the microscopic mechanisms of CO₂ enhancing shale oil recovery remain poorly understood. In this paper, the molecular dynamics simulation method is adopted to investigate the replacement behavior of CO₂ in shale oil reservoirs from a micro perspective. Three kinds of $n$-alkanes are selected as the simulative crude oil in silica nanopores. Molecular dynamics models are established to study the occurrence patterns of different alkanes on the rock surface and the alkane-stripping characteristics of CO₂. The fluid density, mean square displacement and centroid variation are evaluated to reveal the effect of CO₂ on alkanes. The results indicate that different alkanes exhibit varying occurrence characteristics of oil film on the rock surface of the shale reservoir. Specifically, a higher carbon number leads to a thicker oil film. Through the alkane molecular gaps, CO₂ penetrates the alkane molecular system and reaches the rock surface to effectively strip the oil film of different alkane molecules. CO₂ will more readily mix with the stripped oil molecules and displace them from the rock surface when the carbon number is small. The process for CO₂ replacing crude oil on the rock surface can be divided into four typical stages, namely, CO₂ diffusion, competitive adsorption, emulsification and dissolution, and CO₂-alkanes miscible phase (for light alkanes). This study contributes to the improvement of micro-scale enhanced oil recovery mechanisms for shale oil via CO₂ injection and provides a guidance for enhancing shale oil recovery by using CO₂.