Versatile amorphous structures of phosphonate metal–organic framework (pMOF)/alginate composite are proposed to selectively separate alkaline and alkaline earth metal ions. Initially, the gelation of alginate by Al3+ ions provides preconfined Al3+ coordination. The phosphonate organic ligand is subsequently coordinated with Al3+ ions to make pMOF based on the preconfined Al3+ coordination. Al3+−phosphonate organic ligand complexes of pMOF are simultaneously intertwined with Al3+−alginate crosslinks with the aid of partial hydrolysis. Amorphous structures of Al3+‐based pMOF/alginate composite are largely modulated, as the reaction temperature and intertwinement degree of alginate networks vary. In addition, partial hydrolysis plays an important role for amorphization, which gives rise to versatile amorphous structures. The Al3+‐based pMOF/alginate composite is found to have tunable sieving of alkaline and alkaline earth metal ions with varying the degrees of intertwinement of amorphous structures and Al3+−phosphonate organic ligand complexes. In particular, a certain type of amorphous structure can effectively reject Li+ ions with small hydration energy through dehydration. Benefiting from amorphous structures, this work will provide a variety of separation opportunities accompanying unique properties and allow efficient separation of ions and similar‐sized molecules.