This study sought to characterize the differences between the 3D-printed and decellularized tracheal grafts, providing the basis for the synthesis of the more reasonable and effective tissue-engineered trachea. We compared the biomechanical properties and biocompatibility of the 3D-printed tracheal graft and decellularized tracheal graft in vitro and evaluated the biocompatibility, immune rejection and inflammation of the two materials through in vivo implantation experiments. Compared with the decellularized tracheal graft, the 3D-printed tracheal graft was associated with obviously higher biomechanical properties. The results demonstrated enhanced growth of BMSCs in the decellularized tracheal graft compared to the 3D-printed one when co-culture with two tracheal graft groups. Moreover, the CCK-8 assay demonstrated significant cell proliferation on the decellularized tracheal graft. Serum IgG and IgM measured in vivo by implantation testing indicated that the 3D-Printed tracheal graft exhibited the most significant inflammatory response. HE staining indicated that the inflammatory response in the 3D-printed tracheal graft consisted mainly of eosinophils, while little inflammatory cell infiltrates were observed in the decellularized tracheal graft. CD68 immunohistochemical analysis indicated that the infiltration of macrophages was not significant in both tracheal grafts. Our findings suggest that the biomechanical properties of the 3D-printed tracheal grafts are better than the decellularized tracheal grafts. Nonetheless, the decellularized tracheal graft exhibited better biocompatibility than the 3D-printed tracheal graft.