The invention belongs to the technical field of biomaterials, and particularly relates to a preparation method and an application of a high-biocompatibility biodegradable bone filling material. The bone filling material is composed of polyurethane urea having phosphorylcholine at the end of a flexible side chain, and polyurethane urea is prepared from a single-ended dihydroxy polyethylene glycol phosphorylcholine compound, double-ended hydroxypolydioxanone and L-lysine diisocyanate-1,4-dibutyl diamine-L-lysine diisocyanate. The phosphorylcholine group located at the end of the flexible polyethylene glycol side chain is easily enriched on the surface of the material in order to greatly improve the hydrophilicity of the material, hinder the deposition of platelets and proteins and avoid theformation of thrombus, so the material has high biocompatibility, solves the problems of low biocompatibility and poor mechanical performances of polyurethane with the side chain simply being polyethylene glycol or phosphorylcholine, especially used a long-term implant material, in the biomedical field, and has widened applications in fields of tissue engineering, drug controlled release, gene therapy and cosmetics.