The present invention provides a manufacturing method of a semiconductor structure, comprising the following steps. First, a substrate is provided, a first dielectric layer is formed on the substrate, a metal gate is disposed in the first dielectric layer and at least one source/drain region (S/D region) is disposed on two sides of the metal gate, a second dielectric layer is then formed on the first dielectric layer, a first etching process is then performed to form a plurality of first trenches in the first dielectric layer and the second dielectric layer, wherein the first trenches expose each S/D region. Afterwards, a salicide process is performed to form a salicide layer in each first trench, a second etching process is then performed to form a plurality of second trenches in the first dielectric layer and the second dielectric layer, and the second trenches expose the metal gate.