In our previous work, a computational method to characterize framework aluminum in aluminosilicates was proposed (García-Pérez, E., et al. Angew. Chem., Int. Ed. 2007, 46, 276). In this work, the method was adopted to identify the most likely positions of aluminum in TON, FER, and MOR zeolites and to understand their different adsorption behaviors in detail. The simulations show that the location of aluminum affects the positions of the ions, and thus influences the adsorption. With the determined structures, the effects of non-framework ions on the adsorption behaviors of alkanes in these zeolites were studied systematically and the relations of the macroscopic adsorption behaviors of alkanes to their microscopic structures were elucidated. The results provided a better understanding of the influences of the position and density of aluminum on adsorption in zeolites from a microscopic level that may guide the future rational synthesis of new structures.