To explore new 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-derived metal-organic frameworks (MOFs), we employed 2,6-dicarboxyl-1,3,5,7-tetramethyl-8-phenyl-4,4-difluoroboradiazaindacene (H2L) as a ligand to successfully synthesize five coordination polymers, namely, {[Zn2(L)2(bpp)]·2H2O·2EtOH}n (1), {[Cd2(L)2(bpp)]·2H2O·EtOH}n (2), {[Cd2(L)(bpe)3(NO3)2]·2H2O·DMF·EtOH}n (3), {[Cd(L)(bpe)0.5(DMF)(H2O)]}n (4), and {[Cd(L)(bpe)0.5]·1.5H2O·DMF}n (5) (bpp = 1,3-bi(4-pyridyl)propane, bpe = 1,2-bi(4-pyridyl)ethane). Except for two 2D-layer coordination polymers 3 and 4, the rest samples exhibit 3D metal-organic frameworks with certain pore sizes, especially MOFs 1 and 5. Spectroscopic and crystallographic investigations demonstrate that the absorption and emission energies of the BODIPY chromophores are sensitive to the coordination modes. Moreover, in case 2, the transition metal centers coordinated with the dicarboxylate ligands L(2-) are capable of forming the two BODIPY units in coplanar arrangements (θ = 37.9°), simultaneously suppressing the uncommon J-dimer absorption band centered at 705 nm with a long tail into the near-infrared region at room temperature. On the other hand, in comparison with the ligand H2L, the emission of monomer-like BODIPY in case 3 is enhanced in the solid state by a considerably long distance between the parallel BODIPY planes (about 14.0 Å).