High mobility group AT-hook 2 (HMGA2) is an architectural transcription factor that functions as an oncogene in various cancers. Although overexpression of HMGA2 has been reported in several myeloid malignancies, its role varies considerably in different disease contexts. Here, we identified a distinct role of HMGA2 as a mediator of noninfectious pneumonia in myelodysplastic syndrome (MDS). The expression level of in CD34 hematopoietic stem cells and progenitors (HSC/Ps) was significantly associated with the incidence of noninfectious pneumonia, a common systemic complication in patients with MDS. Consistent with this clinical investigation, HMGA2 overexpression in a mouse model of an MDS-associated mutation led to the development of lethal noninfectious pneumonia. Mechanistically, HMGA2 overexpression conferred a megakaryocytic lineage bias to HSC/Ps and contributed to platelet activation in MDS mice. P-selectin-positive activated platelets interacted with MDS clone-derived neutrophils that exhibit increased susceptibility to cell death and formed platelet-neutrophil complexes (PNCs). Both the frequency of PNCs and neutrophil cell death within the lung microenvironment increased in MDS mice overexpressing HMGA2. Genetic inhibition of P-selectin attenuated pulmonary tissue damage in MDS mice. These findings indicate that PNCs could be a new therapeutic target for noninfectious pneumonia in patients with MDS and provide new insights into the mechanistic basis of the systemic complications of MDS.