Dyes are major water pollutants due to their large-scale industrial applications. Dyes adversely impact both aquatic and human health. Thus, they require efficient removal from water bodies. Adsorption is an effective method for removing dyes from polluted water. In this study, we simulated the adsorption of bromophenol blue, methylene blue, and methyl orange by asphaltene and its functionalized version. Adsorption was simulated using molecular dynamics (MD) and density functional theory (DFT) calculations. Our results indicated that functionalized and nonfunctionalized dyes have varying interaction energies depending on the nature of the dye. MD simulations indicated that methylene blue tends to have a stronger interaction with asphaltene than the other dyes. Methyl orange bound more strongly with the functionalized asphaltene (FASP) than with the other dyes. Bromophenol blue dye demonstrated weak interaction with both types of asphaltene. DFT calculations were conducted to understand the nature and strength of the interactions between the dyes and asphaltene. In this study, we also analyzed binding energy, electrostatic potential, frontier molecular orbitals, and noncovalent interactions. The DFT and MD analyses supported the experimental finding that FASP is a better adsorbent of dyes than nonfunctionalized asphaltene.