A series of partially fluorinated (C6F13H-modified) polystyrene-b-1,2-polybutadiene (PS-b1,2-PB) copolymers were prepared by the reaction of a model PS-b-1,2-PB copolymer with n-C6F13I followed by substitution of hydrogen for the iodine by hydrogenolysis. The morphologies and domain spacings of the ordered samples at 120 and 195 °C were determined as a function of C6F13H modification extent using small-angle X-ray scattering (SAXS). From the domain spacings an effective interaction parameter (χeff) between the PS and partially C6F13H-modified 1,2-PB blocks was estimated. The χeff at 120 °C increases significantly with fluorination, from ca. 0.05 (0 mol% C6F13H modification) to ca. 0.75 (80 mol % C6F13H modification). The order-disorder transition temperature (TODT) for a partially C6F13H-modified PS-b-1,2-PB (25 mol %) was determined to be 186 ± 3 °C, using rheology and static birefringence. From self-consistent mean-field theory χeff for this block copolymer is estimated to be 0.16 at TODT, which agrees well with the value of 0.21 estimated from the domain spacing. These estimated interaction parameters demonstrate that a selective perfluoroalkylation approach can strongly enhance the incompatibility of PS-b-1,2-PB copolymers and is a powerful method for examining large regions of the block copolymer phase diagram with a single precursor molecule.