Background Our previous studies showed that the coronary collateral microcirculation reserve (CCMR) in rat hearts is abundant, but the structure is naturally flawed, which preventing it from continuously providing alternative blood flow to the ischemic myocardium. Further research indicated that pigment epithelium-derived factor (PEDF) can induce CCMR vessels remodeling in a manner similar to that of fluid shear stress (FSS), thus improving compensatory blood flow. However, the specific mechanism remained unclear. Methods We established the rat model of PEDF overexpression in the myocardium and the cardiac explant angiogenesis model in matrigel to identify the role of the canonical and non-canonical Notch1 signaling pathway in the process of PEDF-induced CCMR remodeling. Results: We found that pharmaceutical blockage of Notch1 pathway via γ-secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) would effectively abrogate the remodeling process, including the diameter expansion and adherens junctions reorganization of CCMR induced by PEDF. In vitro, western blot and enzyme activity assay analysis indicated that PEDF treatment simultaneously active the canonical Notch1 pathway (NICD/AKT/eNOS/NO) and non-canonical Notch1 pathway (TMD/VE-cadherin-LAR-Trio complex). To our amusement, using L-Nitromonomethylarginine (L-NMMA) acetate to inhibit endothelial nitric oxide synthase (eNOS) activity could significantly block PEDF-induced the diameter expansion of the nascent blood vessels, but it had little effect on the reassembly of adherens junctions. While activation of non-canonical Notch1 pathway seems to be the cause of adherens junctions remodeling. Blocking of the non-canonical Notch1 pathway canceled PEDF-driven adherens junctions assembly. Conclusions We demonstrate the specific mechanism of PEDF-induced native collateral microcirculation remodeling. PEDF can active the canonical Notch1 pathway signaling pathway to promote lumenal remodeling and, Simultaneously, active non-canonical Notch1 signaling pathway responsible for adherens junctions assembly.