Fluorine-containing amphiphilic block copolymers, poly(2-hydroxyethyl vinyl ether)-block-poly(2-(2,2,2-trifluoroethoxy)ethyl vinyl ether)) (poly(HOVE-b-TFEOVE) (m = 78, n = 23)), poly(2-hydroxyethyl vinyl ether)-block-poly(2-(2,2,3,3,3-pentafluoropropoxy)ethyl vinyl ether) (poly(HOVE-b-PFPOVE) (m = 74, n = 22)), and poly(2-hydroxyethyl vinyl ether)-block-poly(2-(2,2,3,3,4,4,4-heptafluorobutoxy)ethyl vinyl ether) (poly(HOVE-b-HFBOVE) (m = 79, n = 19)) were synthesized along with the non-fluorine-containing amphiphilic block copolymer, poly(2-hydroxyethyl vinyl ether)-block-poly(n-butyl vinyl ether) (poly(HOVE-b-NBVE) (m = 70, n = 22)), where m and n are polymerization degrees of hydrophilic segment and hydrophobic segment, respectively. These fluorine-containing block copolymers considerably reduced the surface tension of the aqueous solutions, indicating the high surface activity of the block copolymers. They formed core-shell rodlike and/or core-shell spherical micelles in aqueous solutions, which were evaluated by small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and dynamic light scattering (DLS) analyses. A qualitative trend was observed, that is, the fraction of rodlike micelles increased, as the number of fluorine atoms in a hydrophobic segment increased. The fluorine-containing block copolymer selectively solubilized the hydrophobic fluorinated dye into water phase and the fluorinated dye selectivity increased as the number of the fluorine atoms in the hydrophobic monomer unit increased. Solubilization of a low molecular weight compound strongly affected the copolymer micelle structure, which was also confirmed by SANS, SAXS, and DLS analyses.