A spacer structure and a fabrication method thereof are provided. First and second conductive structures are formed over a substrate. A first patterned dielectric layer is formed to cover the first conductive structure and exposing the second conductive structure. A second dielectric layer is formed to cover the first patterned dielectric layer and an upper surface and sidewalls of the second conductive structure. The second dielectric layer disposed over an upper surface of the first conductive structure and the upper surface of the second conductive structure is removed. The first patterned dielectric layer and the second dielectric layer disposed on sidewalls of the first conductive structure form a first spacer structure, and the second dielectric layer disposed on the sidewalls of the second conductive structure forms a second spacer structure. A width of the first spacer structure is larger than a width of the second spacer structure.