To better investigate the degradation and biocompatibility of waterborne biodegradable polyurethanes for tissue engineering, a series of new waterborne biodegradable polyurethanes (PEGPUs) with low degree of crosslinking was synthesized using IPDI, BDO and L-lysine as hard segments, PCL and PEG as soft segment. The bulk structures and properties of the prepared polyurethanes were characterized by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), tensile mechanical tests and water contact angle (WCA) measurements. The degree of microphase separation was slightly improved because of the lowered crosslinking degree of these PEGPUs in comparison with the high cross-linking degree samples, leading to good mechanical properties, as indicated by DSC and stress-strain data. Moreover, biodegradability of the polyurethanes was evaluated in phosphate buffer solutions (PBS) under different pH values and enzymatic solution at pH 7.4 through weight loss monitoring. The results suggested that the degradation of these PEGPUs was closely related to their bulk and surface properties. And the degradation products didn’t show apparent inhibition effect against fibroblasts ,in vitro,. These studies demonstrated that the waterborne biodegradable polyurethanes could find potential use in soft tissue engineering and tissue regeneration.