The present invention relates to a method for preparing a capsule nanoparticle used in encapsulating hydrophobic medicines, comprising the following steps: (A) providing a biocompatible polymer and an organic solution containing a hydrophobic medicine (B) stirring the organic solution at 3-10°C, and titrating with an alcohol solution, so as to make the biocompatible polymer encapsulate hydrophobic medicine to form a capsule nanoparticle (C) ultrasonic vibrating the capsule nanoparticle at 3-10°C (D) filtering the capsule nanoparticle to an average size controllable in the range of 60-450 nm and (E) lyophilizing the encapsulated particles.