The mechanisms of asphaltene aggregation leading to damage and wellbore plugging are still unknown, which is not conducive to finding effective solutions to the relevant problems of asphaltene precipitation in supercritical CO₂ (scCO₂) enhanced oil recovery processes. Therefore, molecular dynamics simulations were performed on an oil–scCO₂ system to investigate the behavior and mechanism of asphaltene aggregation. The results show that the selective extraction of crude oil in scCO₂ leads to the formation of asphaltene nanoaggregates. The vdW interactions among asphaltenes in scCO₂ are stronger than those under vacuum, which aggravates aggregation. Free energy calculations indicate that the remaining binding energy between asphaltenes in scCO₂ is the driving force of asphaltene aggregation. Interestingly, we observed a two-step process of separation and aggregation for asphaltene nanoaggregates, which demonstrates that the efficiency of inhibiting asphaltene aggregation can be improved by adding an inhibitor in the first step of aggregation in scCO₂ flooding.