A method of manufacturing a semiconductor structure includes: providing a substrate; forming a first conductive layer having a first opening over the substrate; depositing a first dielectric layer over the first conductive layer and covering the first opening; forming a second conductive layer having a second opening over the first dielectric layer; depositing a second dielectric layer over the second conductive layer and covering the second opening; performing an etching operation through the second dielectric layer at the second opening and the first dielectric layer at the first opening to form a first via; and forming a first conductive structure in the first via.