The immoderate growth of intermetallic compound (IMC) at the Cu/Sn bonding interface reduces the reliability of bonding joints, leading to the failure of high-density packaging. Herein, we design a double-layer nanotwinned Cu (d-ntCu) structure composed of the perpendicularly aligned nano-twinned Cu (p-ntCu) as the upper layer and horizontally aligned nano-twinned Cu (h-ntCu) as the lower layer. We study the Cu/Sn bonding interface microstructure evolution to reveal the IMC growth inhibition and void suppression ability of d-ntCu. As a comparison, the interface microstructure evolution of single layer h-ntCu/Sn is also studied. After thermal aging, the growth mode of IMC at the Cu/Sn bonding interface can be divided into two stages, which are caused by the in-situ annealing of the p-ntCu. In the initial stage of aging, the main diffusion path of Cu atoms is twin boundary diffusion, causing a rather fast growth of IMC. After 100 h aging, the twins anneal into large grains, which induce a lower growth rate of IMC due to the bulk diffusion of Cu atoms. Compared with the h-ntCu single layer, the IMC thickness of the d-ntCu is suppressed by 20%. Besides, the bonding interface in d-ntCu/Sn is void-free due to the vacancy-sink effect of twin boundaries. Therefore, using d-ntCu as the substrate can not only control the IMC growth rate but also suppress the formation of voids during aging, which is helpful to achieve high bonding reliability.