The effect of difluorocarbene (CF2) modification on the self-assembly of polystyrene-b-polyisoprene (PS-b-PI) copolymers was investigated. We prepared a set of fully CF2-modified PS-b-PI copolymers (PS-b-FPI) with different molecular weights (8-13 kg/mol) and located their order-disorder transition temperatures (TODT) by rheology and static birefringence. Using both mean-field and fluctuation theory, we determined the temperature dependence of the interaction parameter between the styrene and CF2-modified isoprene segments (χSFI). Two series of polystyrene-b-(partially CF2-modified polyisoprene) (PS-b-(FPI-s-PI)) materials with different levels of CF2 modification were also prepared from the reaction between difluorocarbene and two nearly symmetric PS-b-PI precursors with molecular weights of 18 and 61 kg/mol, respectively. A lamellar morphology was established for all of the PS-b-(FPI-s-PI) copolymers below the TODT by small-angle X-ray scattering (SAXS) and rheology. The effective interaction parameter (χeff) between the PS and FPI-s-PI blocks, calculated from the domain spacing determined by SAXS, passes through a minimum before increasing smoothly by a factor of 4 upon complete CF2 modification. Using the binary interaction model originally developed for homopolymer/copolymer blends, we were able to understand the dependence of the χeff on the CF2-modification extent in a quantitative manner and extracted the three pairwise interaction parameters. Rheology and static birefringence were also used to locate the TODT for the lower molecular weight PS-b-(FPI-s-PI) series. The TODT was found to behave in a manner similar to the χeff: a decrease was observed at initial CF2 modification, and a sharp increase was observed upon further CF2 modification.