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This paper presents a fabrication method of microcapsules encapsulating fluorescent nanoparticles sensitive to an organic liquid, which is potentially applicable to the encapsulation of protein, cell and drug. It uses the supra-molecular self-assembly of a block copolymer at the interface of the stable and controllable droplets of water suspended with fluorescent nanoparticles and the polymer solved organic. The size and uniformity of the microcapsules were examined for the various polymer concentrations by using SEM image analysis. The maximum standard deviation of the produced microcapsules of less than 3.5% was obtained from the microcapsules produced from the same conditions. The inclusion of fluorescent nanoparticles was visualized in the fluorescence microscope and by using TEM image. It is shown that this fabrication method can provide the uniform size microcapsules with a higher inclusion.