Endothelial progenitor cells (EPCs) are widely used for angiogenic therapies, as well as predictive biomarkers to assess cardiovascular disease risk. However, it is unknown that whether overexpressed vitamin D receptor (VDR) in EPCs could help EPCs counteracting atherosclerotic risks. Here, we study intravenous transplantation of genetically modified EPCs over-expressing VDR in regulating endothelial dysfunction and spontaneously arising atherosclerotic plaques of ApoE-deficient mice. Firstly, we found that over-expression of VDR in EPCs could reduce atherosclerotic plaque formation in transplanted ApoE-/- mice. In addition, the concentration of serum HDL-C in ovVDR-EPCs group was much higher than that in control groups (ApoE-/- mice without injection or injected with fresh medium or adenovirus vector). While concentrations of serum total cholesterol, LDL-C, apoB and Lp (a) were negatively correlated with the expression level of VDR. What’s more, improved serum concentration of NO and elevated serum and vessel wall expression of eNOS were observed in ovVDR-EPCs group. Furthermore, reduced expression and activity of MMP2, and elevated expression and activity of TIMP2 were detected in ovVDR-EPCs group. Taken together, intravenous transfusion of EPCs that overexpress VDR significantly inhibited atherosclerosis in ApoE-deficient mice and could be used as a potential method for angiogenic therapy.