A series of molecular dynamics simulations were performed to investigate the effect of aliphatic side-chain length on the aggregation behavior of a model asphaltene in water. We found that the extent of aggregation has a nonmonotonic relationship with the side-chain length. Asphaltene molecules with very short or very long side chains can form dense aggregates, whereas those with intermediate chain lengths cannot. Through analysis of the kinetics and driving forces of the aggregation, the role of the side chains in affecting the aggregation behavior was elucidated. Long side chains hinder the formation of parallel stacking structures of the polyaromatic cores while also favoring aggregation through hydrophobic association. The simulation results reported here can be used to propose appropriate means to reduce the extent of aggregation of asphaltene in the presence of water.