A biodegradable soy protein isolate-based waterborne polyurethane composite sponge (SWPU) was prepared from soy protein isolate (SPI) and polyurethane prepolymer (PUP) by a process involving chemical reaction and freeze-drying. Effects of SPI content (0, 10%, 30%, 50%, 70%) on the micro-structure and physical properties of the composite sponges were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). The results showed that the reaction between -NCO of PUP and -NH2 of SPI formed porous SPI-based WPU composite sponges. The results of the water absorption ratio measurement, solvent resistance measurement and compressive testing showed that water absorption, hydrophilicity, and tensile strength in the dry state of the composite sponges increased with the increase of SPI content. Especially, the tensile strength ranged from 0.3 MPa to 5.5 MPa with the increase in SPI content. The cytocompatibility and biodegradability of the composite sponges were evaluated by in vitro cell culture and in vivo implantation experiments. The results indicated that a certain SPI content in the sponges could promote the adhesion, growth, and proliferation of cells, enhance the cytocompatibility and accelerate the degradation speed of composite sponges. During the in vivo implanting period within 9 months, SWPU-50 sponge containing 50% of SPI brought out the lowest activated inflammatory reaction, most newly-regenerated blood capillaries, and best histocompatibility. All results indicated that SWPU-50 composite sponges had greatest potential for tissue engineering.