Background: Acute Graft-Versus-Host Disease (aGVHD) constitutes a prevalent component after allogeneic hematopoietic stem cell transplantation(allo-HSCT). Among the components of the Bone Marrow(BM)microenvironment, Endothelial Progenitor Cells (EPCs) hold significant importance in hematopoietic-supporting and immune reconstitution in post-transplantation patients. Consequently, a discernible correlation emerges between the impairment of EPCs and the incidence and severity of GVHD. Our recent study has shown impaired EPC function and heightened reactive oxygen species (ROS) levels in aGVHD patients (2018, BJH). Additionally, reduced levels of hypoxia-inducible factor-1α (HIF-1α) and autophagy were observed in BM EPCs from aGVHD patients in comparison to those without GVHD(non-GVHD). HIF-1α is closely linked to ROS generation. Therefore, exploring the role of HIF-1α and autophagy in the development of aGVHD after allo-HSCT is significant. Aims: To conduct a comparative analysis of the functions of EPCs and assess the variations in the expression levels of HIF-1α and autophagy-related proteins between aGVHD and non-GVHD patients. Additionally, the study aims to assess whether the low HIF-1α level is responsible for the autophagy deficiency and mitochondrial dysfunction observed in EPCs of aGVHD patients, and to delineate the specific pathways through which this downregulation influences their capacity of hematopoiesis-supporting. Methods: The current prospective clinical case-matched study included 20 patients with aGVHD and 40 patients without GVHD. BM mononuclear cells(BMMNCs) were cultured as former publications reported. EPCs(CD34+, CD133+, CD309+) were flow-sorted for evaluating apoptosis, ROS, and autophagy levels. SiRNA transfection knocked down HIF-1α in human umbilical vein endothelial cells (HUVECs). Endothelial cells(ECs) gene expression levels were determined using Western blot, RT-qPCR. ECs function was assessed by angiogenesis, Transwell cell migration, CCK-8 cell proliferation, and JC-1 mitochondrial staining. ECs were co-cultured with hematopoietic stem cells (HSCs) for seven days, and HSCs were subjected to colony-forming unit assays and other experiments to evaluate hematopoietic stem cell function. ECs NAD+ and NADH levels were assessed by the kit. Results: Downregulation of autophagy signaling pathway in HUVECs following knockdown of HIF-1α, leading to inhibited cell proliferation, migration, and angiogenesis. Similarly, patients affected by aGVHD exhibited reduced HIF-1α expression, impaired autophagy, and cellular function in EPCs compared to non-GVHD patients. HSCs co-culturing with HUVECs with HIF-1α knockdown and EPCs from aGVHD patients resulted in increased apoptosis, elevated levels of ROS, and impaired colony formation ability. However, intervention with HIF-1α activators Roxadustat, which served to upregulate HIF-1α levels in ECs, activated autophagy, and improved cellular function, also enhanced the hematopoiesis-supporting ability. Furthermore, the knockdown of HIF-1α in HUVECs and EPCs of aGVHD patients led to the abnormal activation of SIRT1 and PARP1 and other NAD+-consuming proteins, which subsequently caused a decrease in NAD+ levels and resulted in abnormal mitochondrial membrane potential. The supplementation of NAD+ precursors, specifically β-nicotinamide mononucleotide, effectively increased NAD+ levels in ECs and restored cellular function. Conclusion: The results revealed that the autophagy deficiency was mediated by reduced expression of HIF-1α in EPCs of patients with aGVHD. The deficiency of autophagy also led to abnormal activation of SIRT1 and PARP1, which in turn affected the levels of NAD+ and mitochondrial membrane potential, ultimately impairing cellular function and hematopoiesis-supporting ability. These molecular changes may be identified as potential contributors to the pathogenesis of aGVHD after allo-HSCT. On the other hand, Roxadustat upregulates HIF-1α expression in ECs, which subsequently enhanced the autophagy level and improved mitochondrial function. As a result, cellular function and hematopoiesis-supporting ability were restored. This promising therapeutic approach highlights a novel strategy for preventing and treating of patients with aGVHD after allo-HSCT.