In order to investigate the aggregation mechanisms of asphaltenes in toluene, a series of molecular dynamics simulations were performed on Violanthrone78-based model asphaltenes with different aliphatic/aromatic ratios. Our simulation results show that the attraction between poly-aromatic cores is the main driving force for asphaltene aggregation in toluene, and that the extent of aggregation is independent of the aliphatic/aromatic ratios. On the other hand, analysis of the aggregated structures indicates that long side chains do hinder the formation of large direct parallel stacking structures. In contrast with water as a solvent, toluene exhibits attractive interactions with both the aliphatic and aromatic regions of the asphaltenes, hence reducing the size and stability of the asphaltene aggregates. Our findings help to elucidate, at a molecular level, the different solubility behaviors of asphaltenes in toluene and in water.