Propylene glycol alginate sodium sulfate-loaded nanoparticles (PSS-NP) has been shown potential to prevent the microvascular endothelial injuries caused by diabetic cardiomyopathy (DCM). In this study, we aimed to investigate the effects of PSS-NP on the dysfunction of cardiac microvascular endothelia in streptozotocin (STZ)-induced DCM rat model. Echocardiographic measurements showed a significant improvement of cardiac function in the PSS-NP-treated group. Our results revealed that the abnormalities of cardiac systolic and diastolic functions were suppressed by the treatments of prostaglandin E1 (PGE1), low molecular weight heparin (LMWH), PSS and PSS-NP. Our comparison analysis indicated that PSS-NP showed the strongest inhibitory effects on microvascular endothelial injuries. Transmission electron microscopy analysis demonstrated that PSS-NP protected the cardiac microvascular endothelium and further improved endothelium dysfunction in DCM rats. ELISA and Western blot assays further showed a high efficiency of improving cardiac microvascular endothelial dysfunction with PSS-NP. Our results demonstrated that PSS-NP increased the protein expression of phosphatidylinositol 3-kinase (PI3K)-p85 and vascular endothelial growth factor (VEGF)-A, and the phosphorylation of protein kinase B (Akt) and endothelial nitric oxide synthase (eNOS), which were involved in the amelioration of cardiac microvascular endothelial dysfunction. These data suggest that PSS-NP may be a novel approach to the treatment the coronary microcirculation disorder diseases such as DCM.