Three Co(II) coordination polymers based on flexible bis(2-dimethylbenzimidazole) and the derivatives of the familiar isophthalate co-ligands, namely [Co(L)(ip)]n (1), [Co2(L)2(nip)2]n (2) and [Co2(L)2(tbip)2·2H2O]n (3) (L = 1,2-bis(2-methylbenzimidazol-1-ylmethyl)benzene, H2ip = isophthalic acid, H2nip = 5-nitroisophthalic acid, H2tbip = 5-tert-butylisophthalic acid) have been synthesized by hydrothermal methods and characterized by elemental analyses, IR spectra, thermogravimetric analyses and single-crystal X-ray diffraction. Both complexes 1 and 2 exhibit a 2-fold interpenetrating 3D network with 66-dia topology, whereas complex 3 is bridged by the L and tbip2− ligands to form a rarely tri-nodal (3,3,5) layer with 3,3,5L18 topology. The results indicate that Co(II) mixed coordination polymers structurally modulated by the substituent effect of isophthalate-involved co-ligands. In addition, the fluorescence and catalytic activity of the complexes for the degradation of methyl orange by the sodium persulfate in a Fenton-like process have been investigated.