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Abstract: The ionothermal synthesis of extra‐large‐pore aluminophosphate zeotype with −CLO topological structure, DNL‐1, was studied by using 1,6‐hexanediamine and several quaternary ammonium compounds with different types of cations and anions as co‐structure‐directing agents (co‐SDAs). The phase selectivity and crystallization process were investigated, and results showed that the crystallization of the −CLO and LTA structures correlated with the alkalinity and concentration, rather than with the structure of the co‐SDA. By combining solid/solution 13C NMR spectroscopy and other characterizations on DNL‐1 obtained with different co‐SDAs, it was demonstrated that the ionic‐liquid cation was unalterably occluded in the structure, whereas occlusion of the co‐SDA cation was not imperative. A plausible crystallization pathway was accordingly deduced, in which alkaline co‐SDA, which acted as an acidity regulator in the ionothermal system, could facilitate the formation of the double‐four‐ring (d4r) unit (Al4P4O20), and influence their subsequent assembly mode around ionic‐liquid cations, and thus, direct the crystallization of −CLO and LTA structures at different concentrations of co‐SDA. [ABSTRACT FROM AUTHOR]