Biodegradable polymers have potential as a scaffold material for making small diameter artery bypass grafts. To resist thrombosis, maintain biocompatibility and enhance the remodeling of the grafts, it is crucial to modify polymer scaffolds so that the grafts have antithrombogenic capacity and allow cell infiltration. In this study, two methods of aminolysis on electrospun poly-L-lactide-co-caprolactone (PLCL) microfiber vascular grafts are compared: plasma treatment method and Fmoc-PEG-diamine insertion method. Both methods successfully inserted amino groups on the polymer graft for heparin conjugation. However, plasma treatment resulted in significantly higher initial heparin density and higher heparin stability on PLCL microfibers than Fmoc-PEG-diamine treatment. In addition, mechanical testing demonstrated that the plasma treatment method maintained PLCL microfiber tensile strength after heparin conjugation. Fmoc-PEG-diamine insertion method compromised the mechanical property due to partial fiber melting and structure disruption. Subcutaneous implantation of the grafts in a rat model showed that heparin coating with both methods promoted cell infiltration. This study provides a rationale to optimize the biomolecule conjugation on electrospun PLCL scaffolds, and will have applications in tissue engineering vascular grafts and other tissues.