An unusual example showing reversible interconversion of chain-like isomers under controlled experimental settings is reported, which illustrates the key role of assembly conditions for the target packing architecture with related properties. The reaction of Mn(II) ions with an organic ligand 2-hydroxypyrimidine-4,6-dicarboxylic acid (H(3)hpdc) at room temperature gives a coordination polymer {[Mn-3(hpdc)(2)(H2O)(6)]center dot 2H(2)O}(n) containing parallel staggered stacking, whereas the reaction under hydrothermal conditions at 150 degrees C affords a compound {[Mn-3(hpdc)(2)(H2O)(6)]center dot H2O}(n) possessing plywood-like stacking. Interestingly, two compounds contain similar one-dimensional chain components with different orientations that can be controlled by thermodynamic factors. Thermally triggered reversible interconversion of the two compounds was verified by X-ray powder, IR, and element analysis. The spin-canted antiferromagnetic behaviors are observed in as-synthesized samples, and the influence of chain orientations on magnetic properties has been detected.