Three-dimensional (3D) printing provides a new approach of fabricating implantable products because it permits a flexible manner to extrude complex and customized shapes of the tissue scaffolds. Compared with other printable biomaterials, the polyurethane elastomer has several merits, including excellent mechanical properties and good biocompatibility. However, some intrinsic behavior, especially its high melting point and slow rate of degradation, hampered its application in 3D printed tissue engineering. Herein, we developed a 3D printable amino acid modified biodegradable waterborne polyurethane (WBPU) using a water-based green chemistry process. The flexibility of this material endows better compliance with tissue during implantation and prevents high modulus transplants from scratching surrounding tissues. The histocompatibility experiments show that the WBPU induces no apparent acute rejection or inflammation in vivo. We successfully fabricated a highly flexible WBPU scaffold by deposition 3D printing technology at a low temperature (50°C ~ 70 °C), and the printed products could support the adhesion and proliferation of chondrocytes and fibroblasts. The printed blocks possessed controllable degradability due to the different amounts of hydrophilic chain extender and did not cause accumulation of acidic products. In addition, we demonstrated that our WBPU is highly applicable for implantable tissue engineering because there is no cytotoxicity during its degradation. Taken together, we envision that this printable WBPU can be used as an alternative biomaterial for tissue engineering with low temperature printing, biodegradability, and compatibility.