PURPOSE: A method for effectively manufacturing polymer nanoparticles coated with phasing and PHA dipolymerase is provided. CONSTITUTION: A composition for forming nanoparticles contains phasing or PHA(polyhydroxyalkanoic acid) depolymerase and poly(3-hydroxybutylate) or poly(3-hydroxybutylate-co-3-hydroxyvalate) biocompatible polymer. The composition further contains anion surfactant or cation surfactant. The phasing is originated from Ralstonia eutropha. The PHA dipolymerase is originated from Hydrogenophaga pseudoflava. A method for manufacturing biocompatible polymer nanoparticls comprises: a process of preparing oil phase solution in which biocompatible polymer is dissolved in organic solvent; and a step of adding a composition for forming nanoparticles in oil phase solution to form emulsion.본 발명은 페이신, PHA 디폴리머라제 등의 단백질을 고분자 약물전달체의 매트릭스 성분으로 사용하기 위한 것으로, 페이신 및 PHA 디폴리머라제로 이루어진 군에서 선택되는 단백질 및 생체적합성 고분자를 포함하는 생체적합성 고분자 나노입자 형성용 조성물, 상기 단백질로 코팅된 약물전달체용 고분자 나노입자, 상기 나노입자에 약물이 담지된 약물전달체 및 이들의 제조 방법에 관한 것이다.