Supercritical cyclohexane (SC-cyclohexane) shows significant advantages in mild operating conditions and the modulation of product distribution. To gain insights into the upgrading process of heavy oil in SC-cyclohexane, the dissolution process of polycyclic aromatic hydrocarbons (PAHs) contained in heavy oil was simulated based on molecular dynamics with the use of naphthalene, benzopyrene, and mixtures of naphthalene and benzopyrene as the model compounds. As indicated by the radial distribution function results, in SC-cyclohexane exhibiting low density, cyclohexane formed a solvent shell around PAHs such that the local concentration was reduced and the aggregation of PAHs was inhibited. The results of the solvation free energy suggested that van der Waals forces between PAHs and cyclohexane were mainly dominant. As revealed by the dissolution process of the model compounds in SC-cyclohexane, a low density and a suitable temperature contributed to the solubilization of PAHs. An appropriate temperature and a low density can be selected for the upgrading reaction to limit coke formation.