Many methods have been utilized to adjust the size of superatomic metal nanoclusters, while tuning the geometric conformations of specific nanoclusters is rare. Here, we demonstrate that conformation variation can be realized by slightly modifying the ligand under maintaining the nuclei number of metal atoms. A series of novel "double-chair" conformation Ln12 (Ln = Sm (1), Eu (2), Gd (3), Tb (4), and Dy (5)) clusters were generated by replacing 3-formylsalicylic acid with 2,3-dihydroxybenzoic acid in the Ln12 nanocluster. Intriguingly, Dy12 displays slow magnetic relaxation at low temperatures, while Gd12 shows a large magnetocaloric effect (MCE) of 35.63 J kg-1 K-1 at 2 K for ΔH = 7 T. Additionally, the introduction of numerous coordination water molecules in these clusters enables Dy12 and Gd12 with high proton conductivity, namely, 2.13 × 10-4 and 3.62 × 10-4 S cm-1 under 358 K and 95% RH humidity conditions.