Supercritical carbon dioxide (scCO2) injection into unconventional shale oil reservoirs is a promising approach to enhancing oil recovery efficiency and mitigating greenhouse gas emissions. The complexity of the oil component and composition in shale reservoirs is attributed to depositional conditions and thermal cracking processes. Additionally, the physical characteristics of the oil components vary significantly due to their complex chemical structures and bonding types. During the CO2 extraction, specific oil components are selectively recovered through preferential interactions with CO2. Investigating the CO2 extraction mechanism is necessary to improve the shale oil recovery. This study introduces an innovative method for examining CO2 extraction by utilizing molecules with different polarities, which capture primary subsurface properties and simulate practical underground conditions during extraction. The grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) methods are employed in this work to reveal the adsorption behavior of particles with different polarities in shale reservoirs under various subsurface environments. These findings indicate that CO2 exhibits a preferential potential for extracting nonpolar molecules over polar ones. Furthermore, based on the dynamic parameters such as the mean square distance (MSD) and self-diffusion coefficient, which reflect particle movement during the extraction process, observe that n-octane (C8H18) is extracted and moves as a bulk phase within nanochannels, while lysine (C6H14N2O2) remains firmly attached to shale surfaces regardless of scCO2 injection conditions. This work elucidates the significant impact of scCO2 injection in shales and provides comprehensive insights into microscopic fluid flow dynamics and recovery mechanisms at the atomic level for low-carbon energy development. Overall, this study offers valuable contributions to understanding the complex processes in shale extraction.