The initiation mechanisms of the MTO process over silicoaluminophosphate (SAPO) catalysts with zeolite-like structures using first-principles calculations have been investigated. The supramolecular system of silicoaluminophosphates consisting of inorganic cages with Brønsted acid sites and trapped organic compounds was used as a catalyst in the MTO reaction. To study the structure-property relationship in more detail, the effect of acidity and cage size of different types of SAPOs (SAPO-18, SAPO-34, and SAPO-17 with CHA, AEI, and ERI structures, respectively) in the aromatic cycle of hydrocarbon pool mechanism was investigated. The differences in reaction barriers can be explained by the cage size, pore topology, and environment of framework protons of materials. Product selectivity was controlled by using cavity-type zeolite, the steric constraint of the cavity for the formation of critical intermediates, and acidic strength. The results show that ethylene selectivity increases as the cavity size decreases, and the elliptical pore size of the structures decreases, thereby decreasing the acidity of the zeolite structure, leading to an increase in propylene selectivity. SAPO-18 exhibits the longest reaction lifetime and has the highest amount of carbonaceous material after reaction completion. SAPO-17 with small pore and cavity size is selective to ethylene, although it shows a rapid catalyst deactivation rate.