Most current models used for modeling the pulmonary drug absorption, transport, and retention are 0D compartmental models where the airways are generally split into the airways and alveolar sections. Such block models deliver low fidelity solutions and the spatial lung drug concentrations cannot be obtained. Other approaches use high fidelity CFD models with limited capabilities due to their exorbitant computational cost. Recently, we presented a novel, fast-running and robust quasi-3D (Q3D) model for modeling the pulmonary airflow. This Q3D method preserved the 3D lung geometry, delivered extremely accurate solutions, and was 25 000 times faster in comparison to the CFD methods. In this paper, we present a Q3D-compartment multiscale combination to model the pulmonary drug absorption, transport, and retention. The initial deposition is obtained from CFD simulations. The lung absorption compartment model of Yu and Rosania is adapted to this multiscale format. The lung is modeled in the Q3D format till the eighth airway generation. The remainder of the lung along with the systemic circulation and elimination processes was modeled using compartments. The Q3D model is further adapted, by allowing for various heterogeneous annular lung layers. This allows us to model the drug transport across the layers and along the lung. Using this multiscale model, the spatiotemporal drug concentrations in the different lung layers and the temporal concentration in the plasma are obtained. The concentration profile in the plasma was found to be better aligned with the experimental findings in comparison with compartmental model for the standard test cases. Thus, this multiscale model can be used to optimize the target-specific drug delivery and increase the localized bioavailability, thereby facilitating applications from the bench to bedside for various patient/lung-disease variations.