Due to the small differences in the chemical properties of facial (fac) and meridional (mer) stereoisomers, selective synthesis of one of the isomers is challenging, especially for lanthanide complexes. By using a flexible bidentate phosphine oxide ligand, we managed to isolate three stereoisomeric 2D and 3D coordination polymers, in which six-coordinate Dy(III) ions possess fac- or mer-Cl3O3 coordination environments. Structural studies indicate that the stereochemistry differences result from their various supramolecular interactions (e.g., hydrogen bonding and π⋯π stacking). Magnetic property measurements reveal the different static and dynamic magnetic behaviours of the three stereoisomers. Ab initio CASSCF calculations were then performed which indicated that their distinct magnetic behaviours arise from their fac/mer configurations. Compared to fac-Dy(III), mer-Dy(III) possesses more axial ground-state KDs and higher first excited KDs.