In this article, we report the design, synthesis, and characterization of a series of cyclometalated iridium(III) polypyridine complexes containing a perfluorobiphenyl (PFBP) moiety [Ir((NC)-C-boolean AND)(2) (bpy-PFBP)](PF6) (bpy-PFBP = 4-(S-(perfluoro- (1,1' -biphenyl)-4-yl)-N-mercaptoethylaminocarbonyloxy-methyl) -4' -methyl- 2,2' -bipyridine; (HNC)-C-boolean AND = 2-phenylpyridine (Hppy) (1a), 2- (4-hydrox ymethylphenyl)pyridine (Hppy-CH2OH) (2a), 2-((1,1'-biphenyl)-4-yOpyridine (Hpppy) (3a), 2((4'-hydroxymethyl-1,1'-biphenyl)-4-yl)pyridine (Hpppy-CH2OH) (4a), 2-phenylquinoline (Hpq) (5a), 2-(4-hydroxymethylphenyl)quinoline (Hpq-CH2OH) (6a)). Their PFBP-free counterparts [Ir((NC)-C-boolean AND) 2 (bpy-C4)](PF6) (bpy-C4 = 4-(N-n-butylaminocarbonyloxymethyl)-4'-methy1-2,2'-bipyridine; (HNC)-C-boolean AND = Hppy (1b), Hppy-CH2OH (2b), Hpppy (3b), Hpppy-CH2OH (4b), Hpq (5b), Hpq-CH2OH (6b)) were also prepared for comparison studies. Upon irradiation, all the complexes displayed intense and long-lived greenish-yellow to orange luminescence in solutions under ambient conditions and in low-temperature alcohol glass. Reactions of the PFBP complexes with peptides containing the FCPF sequence via the pi-clamp-mediated cysteine conjugation afforded luminescent peptide conjugates that exhibited rich photophysical properties. Using complex 3a as an example, we demonstrated that the conjugation of complexes to organelle-targeting peptides is an effective means to modulate their intracellular localization behavior, which was further shown to be important to their performance in photodynamic therapy. The results of this work will contribute to the development of photofunctional transition metal complexes as theranostic agents.