The aim is to investigate the clinical efficacy of Alprostadil in diabetes mellitus (DM) combined with peripheral atherosclerosis and to investigate the molecular mechanisms. Patients included 154 cases with DM combined with peripheral atherosclerosis and were divided into the conventional group (77 cases) and the Alprostadil group (77 cases). Both groups of patients were given conventional treatment, and the Alprostadil group was given Alprostadil treatment on the basis of the conventional group. The therapeutic efficacy and clinical symptom improvement were compared, and the adverse reactions were observed. An in vitro cell model was constructed using high glucose (HG) (50 mM) and oxidized low-density lipoprotein (50 μg/mL) treatment. The total effective rate of treatment in the Alprostadil group was higher than that in the conventional group. The biochemical indices of whole blood viscosity, plasma viscosity, erythrocyte pressure volume, and fibrinogen, as well as the level of inflammatory factors in the Alprostadil group were lower than those in the conventional group. The incidence rate of adverse reactions of Alprostadil administration was lower than that in the conventional group (P = .030). Alprostadil inhibited platelet aggregation and promoted platelet spreading. Alprostadil had an ameliorative effect on HG- and oxidized low-density lipoprotein cholesterol (ox-LDL)-induced human umbilical vascular endothelial cells (HUVECs), and promoted apoptosis and inflammatory response of HUVECs. Clinically, the use of Alprostadil as an adjunct to conventional therapy for the treatment of DM combined with peripheral atherosclerosis has high clinical efficacy. In addition, Alprostadil has a significant ameliorative effect on high glucose- and ox-LDL-induced HUVECs.