A substrate assembly includes a first substrate, a second substrate and a bonding member. The first substrate includes a first surface-modified region having a functionality different from that of a remainder region of the first substrate. The second substrate includes a second surface-modified region connected to the first surface-modified region through a physical interaction and having a functionality different from that of a remainder region of the second substrate. The first and second substrates cooperatively define a space therebetween. The bonding member is disposed within said space to bond said first and second substrates together. A method for bonding substrates is also disclosed.