Waterborne polyurethane (PU) is a green, high performance elastomer but the viscosity of the dispersion is generally too low for direct three-dimensional (3D) printing. Composite brings additional properties while reinforcing the substrate. In the study, printable PU composites were successfully prepared by introducing cellulose nanofibrils (CNFs) and the viscosity was effectively regulated by the amount of neutralizing agent during in-situ synthesis. Rheological measurements supported the good printability. TEM images revealed that CNFs linked multiple PU nanoparticles to form a 'skewer’ structure. PU/CNF scaffolds were 3D-printed with excellent pattern fidelity and structure stability. Meanwhile, the compression modulus was much higher than the scaffolds printed with a water-soluble viscosity enhancer (PEO). Fibroblasts kept proliferating in the scaffolds for two weeks. The interaction between CNF and PU may offer a novel and unique way to tune the viscosity of waterborne PU for direct 3D printing and enhance the properties of the green elastomers.