The present invention provides a manufacturing method of a semiconductor device, at least containing the following steps: first, a substrate is provided, wherein a first dielectric layer is formed on the substrate, at least one metal gate is formed in the first dielectric layer and at least one source drain region (S/D region) is disposed on two sides of the metal gate, at least one first trench is then formed in the first dielectric layer, exposing parts of the S/D region. The manufacturing method for forming the first trench further includes performing a first photolithography process through a first photomask and performing a second photolithography process through a second photomask, and at least one second trench is formed in the first dielectric layer, exposing parts of the metal gate, and finally, a conductive layer is filled in each first trench and each second trench.