Heparin-conjugated biodegradable copolymers were synthesized by attaching heparin to the ends of the copolyesters of ε-caprolactone and L-lactide(PLCL) in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide. They were characterized by means of ~1H NMR, FTIR, XPS and UV-spectrophotometer techniques. The results indicate that heparin is successfully covalently coupled to PLCL, and the heparin-conjugated content is increased with increasing the ε-caprolactone molar content in the copolyesters. The PLCL surface after heparining became more hydrophilic than before due to the decrease of hydrophilic static contact angle. The clotting time of PLCL containing heparin was evaluated by activated partial thromboplastin time(APTT), thrombin time(TT) and prothrombin time(PT) measurements. The antithrombincity of the copolymers modified with heparin was improved among which the sample LC-90-H was the best. Finally, ultrafine fibers of LC-90-H were prepared by electrospinning process. It shows the promise to be applied in the inner-layer of tissue engineering blood vessel scaffolds.