A semiconductor structure and a manufacturing method thereof are provided, wherein the semiconductor structure includes a substrate and gate structures. The gate structures are disposed on the substrate. Each of the gate structures includes a gate, a first spacer and a second spacer. The gate is disposed on the substrate. The first spacer is disposed on a sidewall of the gate. The second spacer is disposed on the first spacer. In a region between two adjacent gate structures, the first spacers are separated from each other, the second spacers are separated from each other, and an upper portion of each of the second spacers has a recess. The semiconductor structure can be used to form a good metal silicide.