Decellularized tissue engineering scaffolds appear to have the properties of similar structure and mechanical characteristics to native tissues，good biocompatibility，suitability for cell adhesion，growth and angiogenesis induction，and non-immunogenicity. Genipin has anti-inflammatory，antithrombotic and antioxidative features which can considerably suppress vascular and endothelial inflammatory activation，increase mechanical strength of biological scaffolds，inhibit inflammatory response and decrease degradation rate of biological scaffolds. By cross-linking with decellularized matrices，Genipin can further improve corresponding performance of tissue engineering matrices，which is very helpful to promote the application of tissue engineering into clinical practice of cardiothoracic surgery. This review focuses on recent research process and possible prospects of Genipin cross-linking in tissue engineering in the field of cardiothoracic surgery.