Coordination complexes, [Co2(1)4(H2O)2] (2), [Ni2(1)4(H2O)2] (3), and [Cu(1)2] (4), by using an asymmetric and partially fluorinated 3-hydroxy-3-pentafluorophenyl-1-phenyl-2-propen-1-one (H1) have been prepared, and the structures were investigated to compare with the corresponding fully fluorinated complexes of [Co2(5)4(H2O)2] (6), [Ni2(5)4(H2O)2] (7), and [Cu(5)2] (8) with bis(pentafluorobenzoyl)methane (H5) and to understand the fluorine-substituted effects. While the coordination mode of the partially fluorinated complexes was quite similar to the fully fluorinated complexes, the intra- and intermolecular π-interactions of the ligand moieties were highly influenced by the fluorination effects; the arene-perfluoroarene interactions were observed in complexes 2 and 3 as a reason of the dinucleation. In this paper, we describe detail structures of the protonated form of the ligand, H1, and complexes 2–4 by X-ray crystallographic studies.