The bioinert characteristic of polycaprolactone (PCL) remains a major defect when using PCL-based materials as small-diameter vascular grafts for implantation in vivo. To improve the hydrophilicity, cytocompatibility, and biodegradation of PCL vascular grafts, we constructed hybrid vascular grafts from electrospun PCL/gelatin. The PCL/gelatin hybrid vascular graft was further functionalized with the addition of heparin, to improve hemocompatibility. This study investigated the performance of heparin-loaded PCL/gelatin hybrid vascular grafts in vivo. Our results showed that the combination of gelatin and PCL was an effective approach to overcome each individual component's shortcomings, in the context of vascular graft generation. Furthermore, by loading heparin onto the grafts, thrombosis, which could be otherwise induced by gelatin, was prevented. Overall, our electrospun heparin-loaded PCL/gelatin vascular grafts promoted endothelialization and regulated smooth muscle regeneration. The data presented here show PCL/gelatin and heparin-loaded vascular grafts as an effective biomaterial candidate for the generation of artificial small-diameter vascular grafts.