An interconnect structure has a substrate having devices already formed thereon. A dielectric layer covers over the substrate. A conductive structure having at least two substructure separated by an air gap is formed on the dielectric layer. A capping layer covers the conductive structure and the air gap. The capping layer at a portion above the air gap also fills into the air gap by a predetermined distance. The air gap may also extend into the dielectric layer to have a greater height. An etching stop layer is formed on the capping layer. An inter-metal dielectric layer is formed on the etching stop layer. The inter-metal dielectric layer, the etching stop layer and the capping layer are patterned to form an opening that exposes a top surface of the conductive structure. The opening may also expose a top portion of a sidewall of the conductive structure if a misalignment occurs, but the opening does not expose the air gap due to protection from the predetermined distance of the capping layer within the air gap. A next level of conductive structure can be formed to fill the opening. A liner layer can be also formed on a sidewall of the substructure interfacing the air gap, so as to protect the conductive structure.