This study focuses on evaluating the differences between describing the asphaltene fraction using a unique average molecular structure compared to a multistructural approach by examining its effects on aggregation behavior using molecular dynamics (MD). Three asphaltene representations were considered: a hydrocarbon skeleton (without heteroatoms), a single average asphaltene molecular structure (with heteroatoms), and a multistructural approach (several molecular structures with different characteristics and heteroatom contents). Representative aromatic and resin molecules were also employed to describe the maltene content. In total, four systems were evaluated by MD simulations: the three asphaltene representations dissolved in Heptol-50 (1:1 mixture of n-heptane and toluene) at a concentration of 7 wt %, as well as the multistructural representation of asphaltenes dissolved in its respective maltene. Asphaltene aggregation behavior was assessed by using the radial distribution function (RDF), the asphaltene− asphaltene interaction energies, and the size distribution of the asphaltene aggregates. Our results showed that a multistructural approach to describing asphaltenes could more accurately reproduce the elemental analysis data than the conventional unistructural approach. In addition, the size of the asphaltene aggregates was found to double when a multistructural representation was used compared to a unistructural approach. Furthermore, heteroatom content increased the average size of the asphaltene aggregates by a factor of 1.5. Interestingly, maltenes reduced aggregate sizes by a factor of 0.4, presumably due to the role of the resins and the structure of the aromatic compounds proposed for the synthetic crude oil. Consequently, this study presents a promising approach to describe the complexity of oil by using a multistructural representation of the asphaltenes, which can be extensively implemented in molecular dynamics studies.