Hydrophilic drugs can be delivered into lungs via nebulization for both local and systemic therapies. Once inhaled, ultrafine nanodroplets preferentially deposit in the alveolar region, where they first interact with the pulmonary surfactant (PS) layer, with nature of the interaction determining both efficiency of the pulmonary drug delivery and extent of the PS perturbation. Here, we demonstrate by molecular dynamics simulations the transport of nanodroplets across the PS layer being improved by lipid coating. In the absence of lipids, bare nanodroplets deposit at the PS layer to release drugs that can be directly translocated across the PS layer. The translocation is quicker under higher surface tensions but at the cost of opening pores that disrupt the ultrastructure of the PS layer. When the PS layer is compressed to lower surface tensions, the nanodroplet prompts collapse of the PS layer to induce severe PS perturbation. By coating the nanodroplet with lipids, the disturbance of the nanodroplet on the PS layer can be reduced. Moreover, the lipid-coated nanodroplet can be readily wrapped by the PS layer to form vesicular structures, which are expected to fuse with the cell membrane to release drugs into secondary organs. Properties of drug bioavailability, controlled drug release, and enzymatic tolerance in real systems could be improved by lipid coating on nanodroplets. Our results provide useful guidelines for the molecular design of nanodroplets as carriers for the pulmonary drug delivery.