A chemically tailored high-χ block copolymer (BCP), polystyrene-block-poly[2-hydroxy-3-(2,2,2-trifluoroethylsulfanyl)propyl methacrylate] (PS-b-PHFMA), was designed to incorporate tailored surface affinities and chemical incompatibilities for engineering perpendicular lamellae using thermal annealing. PS-b-PHFMA was synthesized via the sequential anionic polymerization of styrene and glycidyl methacrylate and the post-polymerization functionalization of the glycidyl moieties with 2,2,2-trifluoroethanethiol. The bulk studies revealed lamellae with a minimum domain spacing of 9.6 nm and a large effective Flory–Huggins interaction parameter (χeff) of 0.191 at 25 °C. Furthermore, atomic force microscopy and scanning electron microscopy showed perpendicular lamellae of the PS-b-PHFMA prepared on thermally-annealed thin films. The introduction of hydrophobic trifluoroethyl moieties onto the hydrophilic glycidyl moieties successfully balanced the surface affinity of the PHFMA block relative to PS, while simultaneously increasing the strength of segregation. Thus, χeff of the chemically tailored BCP increased, and a perpendicular orientation was facilitated on the thin films using thermal annealing.