Nanoemulsions are useful as drug carriers. Conjugating targeting molecules to nanoemulsions would expand their application to the cell-specific delivery of drugs. Click reactions, such as the Cu (I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC) reaction, are a convenient tool for such functionalization as the conjugation of label or targeting molecules. In this study, we sought to synthesize siloxane-based amphiphilic polymers containing alkyne moieties to form nanoemulsions capable of conjugating azide-functionalized labels by the CuAAC reaction. The siloxane-based homopolymer (P1) and copolymer with polydimethylsiloxane (P2) containing chloropropyl groups were reacted with an imidazole derivative that had an ethynyl group at the 1-position to generate PIm1 and PIm2, respectively. PIm1 and PIm2 exhibited good solubility in polar solvents such as methanol, dimethylformamide, dimethyl sulfoxide and H2O. Further, PIm2 exhibited solubility in chloroform and dichloromethane. Azide-functionalized fluorescent dyes and green fluorescent proteins were conjugated with PIm1 and PIm2 by the CuAAC reaction. The labeled polymer emulsified soybean oil in water to form emulsions. The average emulsion size was 150 nm. The fluorescent labels on the emulsions were successfully observed with a fluorescent microscope. Conjugation of PIm1 and PIm2 with targeting molecules by the click reaction would be useful for cell-specific drug delivery.