A bump structure with multiple layers may include a first layer electrically connected to a protective substrate hermetically packaging a base substrate, the first layer allowing the base substrate and the protective substrate to be spaced apart from each other at a predetermined distance; and a second layer electrically connected to the first layer, the second layer being eutectically bonded on a surface of the base substrate. The first layer may have a melting point higher than a eutectic temperature of the second layer and the base substrate. When using a bump structure with multiple layers, it is possible to secure a space in which a micro-structure such as a microelectromechanical systems (MEMS) device on a base substrate may be driven. Further, it is possible to prevent a contact between adjacent structures or electrodes from being generated due to diffusion of a bonding material in a hermetical packaging process.