Asphalt has been the primary material for pavements and other building components such as roof shingles and waterproofing systems, which can be the path for stormwater runoff pollutants such as heavy metals (HMs). In this study, the capability and mechanism of asphalt and biochar-modified asphalt (BMA) to remove Cu as the typical HM found in the road dust and surface runoff were fundamentally explored for the first time. Experiment and multiscale molecular simulations were performed. Molecular dynamics (MD) simulations showed the Cu absorption into the asphalts. Monte Carlo (MC) and density functional theory (DFT) revealed the detailed mechanism of Cu absorption. Biochar (BC) presence modified the spatial distribution of maltene and asphaltene fractions in asphalt and enhanced the absorption. Maltenes were absorbed into the porous structure of BC, leaving more asphaltenes in the asphalt part of BMA. Asphaltenes were the Cu adsorbing preference sites ascribed to the cation-π interaction between Cu and the aromatic plane. The DFT simulations also suggested favourable adsorption of other commonly found metals (e.g., Cr, Pb, Ni, Cd, and Zn) onto asphaltenes. The present study found the capability and mechanism of BMA and asphalt to remove HMs at the molecular scales, providing a path for designing asphalts with value-added functionality in minimizing environmental pollution.