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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} (<b>1</b>) (L = tris(2-benzimidazolylmethyl) amine) consisting of <i>π</i>-stacked cubes which are assembled from eight partially protonated L ligands is obtained. By soaking the crystals of compound <b>1</b> in 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} (<b>2</b>).