A spacer structure and a fabrication method thereof are provided. The method includes the following operations. First and second conductive structures are formed over a substrate. Dielectric layer is formed to cover the first and second conductive structures. Hard mask layer is formed over the dielectric layer. The hard mask layer covers the dielectric layer over the first conductive structure, and the hard mask layer has an opening exposing the dielectric layer over the second conductive structure. The dielectric layer exposed by the hard mask layer is etched to reduce thickness of the dielectric layer. The hard mask layer is removed. The dielectric layer is etched to form first main spacer on sidewall of the first conductive structure and second main spacer on sidewall of the second conductive structure. A first width of the first main spacer is greater than a second width of the second main spacer.