Dysfunction of endothelial progenitor cells (EPC) contribute to diabetic vascular disease. MicroRNAs (miRNAs) are key regulators of diverse cellular processes, including angiogenesis. We recently reported that downregulated miR‐130a in patients with Type 2 diabetes mellitus (DM) results in EPC dysfunction, including increased apoptosis, likely via its target runt‐related transcription factor 3 (Runx3). However, whether miR‐130a affects the autophagy of EPC is unknown. The aim of the present study was to explore the effects of miR‐130a on the autophagy and cell death of EPC, as well as their expression of Beclin 1 (BECN1; an initiator of autophagosome formation) and the anti‐apoptotic protein Bcl2 (which binds to and inactivates BECN1), and the role of Runx3 in mediating these effects. The EPC were cultured from peripheral blood mononuclear cells of diabetic patients and non‐diabetic controls. Cells were transfected with an miR‐130a inhibitor, or mimic‐miR‐130a or mimic‐miR‐130a plus lentiviral vector expressing Runx3 to manipulate miR‐130a and/or Runx3 levels. The number of autophagosomes was counted under transmission electron microscopy and cell death was examined by flow cytometry. The mRNA expression of Beclin1 was measured by real‐time polymerase chain reaction and the protein expression of Beclin1 and Bcl2 was determined by western blotting. Both the number of autophagosomes and Beclin1 expression were increased in EPC from patients with DM. Inhibition of miR‐130a increased the number of autophagosomes and Beclin1 expression, but attenuated Bcl2 expression. Overexpression of miR‐130a decreased the number of autophagosomes, cell death and Beclin1 expression, but promoted Bcl2 expression; these effects were mediated by Runx3. In conclusion, miR‐130a is important for maintaining normal autophagy levels and promoting the survival of EPC via regulation of Bcl‐2 and Beclin1 expression, via Runx3. MiR‐130a may be a regulator linking apoptosis and the autophagy of EPC.