Heavy organic matter deposition risk during CO2 injection in shale oil reservoirs cannot be ignored. Clarifying the microscopic mechanism of heavy organic matter deposition during CO2 injection in shale oil reservoirs is the key to accurately predicting the risk of heavy organic matter deposition. The representative organic pore models were constructed based on the structural characteristics of shale matrix nanopores. Equilibrium molecular dynamics (EMD) and grand canonical Monte Carlo (GCMC) simulation methods were adopted to investigate the storage mechanism and influencing factors of hydrocarbon components in shale nanopores and the effect of CO2 injection on the distribution of hydrocarbon components. The simulation results indicated that heavy hydrocarbon components were mainly distributed in the adsorbed state near the pore wall. Light components were mainly distributed in the central area of the pores as the free state in organic pores. CO2 extraction of light components in shale oil will destroy the stable structure of colloidal asphaltene. Heavy organic matter molecules will associate and deposit by the π-π stacking effect between aromatic cores and finally adsorb in nanopore walls of the shale matrix. In addition, CO2 injection can replace part of the adsorbed methane and ethane, and the microporous space in the kerogen matrix is the main space for CO2 geological storage. The research results reveal the microscopic mechanism of heavy organic matter deposition during CO2 injection in shale oil reservoirs.