Emulsion electrospinning is a convenient and promising method for incorporating proteins and drugs into nanofiber scaffolds. The aim of this study was to fabricate a nanofiber scaffold for anticoagulation and rapid endothelialization. For this purpose, we encapsulated heparin and vascular endothelial growth factor (VEGF) into the core of poly(L-lactic acid-co-ɛ-caprolactone) (P(LLA-CL)) core-shell nanofibers via emulsion electrospinning. The fiber morphology, core-shell structure and hydrophilicity of the nanofiber mats were analyzed by scanning electron microscopy, transmission electron microscopy and water contact angle. The blood compatibility was measured by hemolysis and anticoagulation testing. A CCK-8 assay was performed to study the promotion of endothelial progenitor cell (EPC) growth and was complemented by immunofluorescent staining and SEM. Our study demonstrates that heparin and VEGF can be incorporated into P(LLA-CL) nanofibers via emulsion. The released heparin performed well as an anticoagulant, and the released VEGF promoted EPC growth on the fiber scaffolds. These results imply that electrospun P(LLA-CL) nanofibers containing heparin and VEGF have great potential in the development of vascular grafts in cases where antithrombogenicity and accelerated endothelialization are desirable.