Biodegradable elastomers in the form of polyurethane nanoparticles (NPs) were successfully synthesized based on the combinations of two hydrolysis-prone polyester diols by a green water-based process. The anionic nature of the polymers successfully rendered polyurethane NPs (30-50 nm) consisting of approximately 200-300 polymer chains. The mechanical properties and degradation rate could be adjusted by the types and ratios of the component oligodiols in the soft segment. We demonstrated the feasibility using these biodegradable NPs as building blocks to generate self-assembled morphologies in nanometric, micrometric, or bulk scale, bearing excellent elasticity and biocompatibility. The elastic NPs and their various assembled forms represent a series of smart biodegradable elastomers with potential medical applications.