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 C 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 (Al P O ), 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.