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To investigate the sequentially plasma-activated bonding (SPAB) mechanism of silicon/silicon wafers, the surface hydrophilicity, and the interface voids, nanostructures and chemical compositions that control the bonding quality, such as bonding strength, have been observed. Although the sequentially plasma-activated surfaces are hydrophilic, the SPAB mechanism is not identical to the hydrophilic bonding. SPAB shows high bonding strength at room temperature and water rearrangement below 150°C, which removes the water from the interface to the bulk. This results in a thinner amorphous silicon oxide layer at the interface. Further heating of the bonded wafers desorbs water from the bulk. The heating at 225°C starts producing hillocks at the interface, which turn into voids at temperatures above 400°C for absorbing the hydrogen gas produced from the desorbed water at the interface. The new and bigger voids are due to the hydrogen gas at 600°C and start accumulating at 800°C, resulting in bubbles caused by the accumulation of voids at the preferential sites. No nitrogen exists either in silicon or in the amorphous SiO2 layer at the interface. The Si-L2, 3 edges from the amorphous silicon oxide at the bonded interface are identical to those of the standard SiO2.