Pulmonary delivery is an effective drug delivery strategy for the treatment of local respiratory diseases. However, the rapid systemic absorption through the lung due to the thin barrier and persistent lung clearances influence the drug retention in the lung. In this study, we designed a lipid-coated genistein nanocrystals (Lipo-NCs) formulation to achieve enhanced efficiency of local pulmonary delivery. The Lipo-NCs were fabricated by modifying genistein nanocrystals (NCs) with phospholipid membrane through thin film hydration following the homogenization method. The prepared Lipo-NCs exhibited a decreased drug release rate compared with the naked NCs. Our results demonstrated that intracellular uptake and transcellular transport of NCs by the Calu-3 epithelial layer were reduced after lipid coating. Furthermore, the macrophages clearance was also impeded by this Lipo-NCs formulation. In vivo lung retention and distribution revealed that more genistein was retained in the lung after intratracheal administration of Lipo-NCs. The pharmacokinetic study displayed that the AUC_(0-t) values of Lipo-NCs were 1.59-fold lesser than those of the NCs group, indicating a reduced systemic absorption. In conclusion, this research indicated that Lipo-NCs could be a suitable formulation for reducing systemic absorption and macrophages clearance, and thus enhancing drug concentration in lung by pulmonary delivery.