Background: Mesenchymal stem cells (MSCs) may contribute to repair in severe diseases including acute lung injury (ALI). However, applications with MSCs have been restricted due to safety considerations and limitations in terms of large-scale production and industrial delivery. Alternatively, the MSC secretome has been considered promising for use in therapeutic approaches and has been advanced to pre-clinical and clinical trials. Furthermore, the MSC secretome can be freeze-dried into a stable and ready-to-use supernatant lyophilized powder (SLP) form.Methods: Intratracheal bleomycin was used to induce ALI in mice, and intratracheal MSC SLP was delivered as a treatment. Histopathological assessment was achieved by hematoxylin and eosin, immunohistochemistry, and immunofluorescence staining. Apoptosis, inflammatory infiltration, immunological cell counts, cytokine levels, and mRNA- and protein-expression levels of relevant targets were measured by performing terminal deoxynucleotidyl transferase dUTP nick-end labeling assays, determining total cell and protein levels in bronchoalveolar lavage fluids, flow cytometry, multiple cytokine-detection techniques, and reverse transcriptase-quantitative polymerase chain reaction and western blot analysis, respectively. Plasma lipid profiles were detected by performing lipidomics analysis.Results: Here, we found that intratracheal MSC SLP considerably promoted cell survival, inhibited epithelial cell apoptosis, attenuated inflammatory cell recruitment, and reversed immunological imbalances induced by bleomycin. MSC SLP inhibited signaling through the interleukin 6–phosphorylated signal transducer and activator of transcription pathway to activate tumor protein 63–jagged 2 signaling in basal cells, suppress T helper 17 cell differentiation, promote p63+ cell proliferation and lung damage repair, and relieve inflammatory responses. Furthermore, MSC SLP significantly reversed changes in plasma lipid profiles caused by bleomycin.Conclusions: MSC SLP ameliorated ALI by activating p63 and promoting p63+ cell proliferation and the repair of damaged epithelial cells. The findings of this study also shed insight into ALI pathogenesis and imply that MSC SLP shows considerable therapeutic promise for treating ALI and acute respiratory distress syndrome. Our findings also suggest that phosphatidylserine has potential for serving as a pharmaceutical or dietary supplement for alleviating ALI.