Aluminum-based flameless ration heaters (AFRHs) are heating elements in food packaging. Water is used to activate AFRHs. The material properties of each region of AFRHs were determined by X-ray diffraction, scanning electron microscopy, and hydrogen and heat generation. The results show that the internal cross-section shows stratification with hydrogen and heat production capacities of 105.2 ± 9.7 mL/g and 1435.0 ± 30.3 J/g for the outer layer, 27.1 ± 4.4 mL/g and 80.4 ± 3.1 J/g for the inner layer, and 1.1 ± 0.01 mL/g and 1.2 ± 0.05 J/g for the middle layer, respectively. According to the correspondence between aluminum and hydrogen in the aluminum-water reaction relationship, the reaction efficiency of the outer layer and the inner layer is as low as 64 and 80%, which is an indication of low reaction efficiency. To analyze the reasons for low reaction efficiency, a pore channel model of 3.5 nm tricalcium aluminate (C3A) was developed using molecular dynamics (MD) to reveal the adsorption behavior of the activator in the pore channel. The results show that the activator is subject to solid surface adsorption in the pore channel with a low diffusion coefficient. Oxygen atoms on the surface adsorb hydrogen atoms to form hydrogen bonds and sodium ions to form ionic bonds with calcium ions. This increases the retention time of the activator on the surface. The MD results explain the low reaction efficiency of AFRHs at the microscopic scale. Moreover, it provides ideas and a basis for the optimization of AFRHs.