Three new isomorphic coordination polymers of Co2+, Zn2+ ions with flexible multicarboxylic acid ligand of the cis,cis,cis-1,2,3,4-cyclopentanetetracarboxylic acid (H4L), [Co4L2(H2O)8]·3H2O (1), [Zn4L2(H2O)8]·3H2O (2) and [Co0.8Zn3.2L2(H2O)8]·3H2O (3), have been synthesized under hydrothermal conditions and by means of controlling the pH of the reaction mixtures (with an initial pH of 6.0 for 1, 4.0 for 2, and 5.0 for 3, respectively). In the crystal of 1, two crystallographically different Co2+ ions (Co1 and Co2) form a negatively-charged coordination polymeric chain, which contains a centrosymmetric, linear, trinuclear Co2+ cluster (Co3L2) subunit; another crystallographically independent Co2+ ion (Co3) coordinated to six water molecules acts as a counter ions to link the neighboring coordination polymeric chains via intermolecular H-bond interactions. The Co2+ ions in 1 were completely and partially replaced by Zn2+ ions to give 2 and 3, respectively. Complex 3 shows a novel molecular alloy nature, due to the random distributions of the Co2+ and Zn2+ ions. Three isomorphic complexes exhibit distinct thermal decomposition mechanisms. The deprotonated cis,cis,cis-1,2,3,4-cyclopentanetetracarboxylic acid ligands decompose at 420–750 °C to give the residue CoO in 1, ZnO + C in 2 and CoO + ZnO in 3. Complex 1 shows a complicated magnetic behavior with co-existence of antiferromagnetic exchange interactions between neighboring Co2+ ions as well as strong spin–orbital coupling interactions for each Co2+ ion; complex 3 exhibits a magnetically isolated high-spin Co2+ ion behavior with strong spin–orbital coupling interactions.