A first bonding material layer is formed on a first substrate and a second bonding material layer is formed on a second substrate. The first and second bonding material layers include a metal. Ions are implanted into the first and second bonding material layers to induce structural damages in the in the first and second bonding material layers. The first and second substrates are bonded by forming a physical contact between the first and second bonding material layers. The structural damages in the first and second bonding material layers enhance diffusion of materials across the interface between the first and second bonding material layers to form a bonded material layer in which metal grains are present across the bonding interface, thereby providing a high adhesion strength across the first and second substrates.