Abstract Displacement height (d $d$) and, particularly, roughness length (z0 ${z}{0}$) are essential urban aerodynamic parameters for earth system modeling the climatic impact of urbanization. Urban heterogeneities, inherent to real cities and impacting significantly the transfer of energy, mass and momentum, are missing or empirically represented without physical basis in the current aerodynamic parameterizations. We propose to account for urban heterogeneities by applying multi‐layer division and the drag‐force approach jointly to urban canopies. The impact of urban heterogeneities is represented by vertical profiles of roughness density to form a physics‐based aerodynamic parameterization for real urban surfaces (denoted RUR). Evaluation over real urban surfaces shows that RUR generally outperforms the classical schemes, especially for the estimate of z0 ${z}{0}$. The enhanced estimates of z0 ${z}_{0}$ from RUR can significantly improve surface flux estimation, especially for relatively rough urban surfaces. This indicates the potential to advance earth system modeling research on the climatic impact of urbanization.