Single-crystal-to-single-crystal metalation of organic ligands represents a novel method to prepare metal–organic complexes, but remains challenging. Herein, a hierarchical self-assembly {(H12L8)·([N(C2H5)4]+)3·(ClO4−)15·(H2O)32} (1) (L = tris(2-benzimidazolylmethyl) amine) consisting ofπ-stacked cubes which are assembled from eight partially protonated L ligands is obtained. By soaking the crystals of compound1in the aqueous solution of Co(SCN)2, the ligands coordinate with Co2+ions stoichiometrically and ClO4−exchange with SCN−via single-crystal-to-single-crystal transformation, leading to {([CoSCNL]+)8·([NC8H20]+)3·(SCN)11·(H2O)13} (2).