A fabricating method of a shallow trench isolation structure includes the following steps. Firstly, a substrate is provided, wherein a high voltage device area is defined in the substrate. Then, a first etching process is performed to partially remove the substrate, thereby forming a preliminary shallow trench in the high voltage device area. Then, a second etching process is performed to further remove the substrate corresponding to the preliminary shallow trench, thereby forming a first shallow trench in the high voltage device area. Afterwards, a dielectric material is filled in the first shallow trench, thereby forming a first shallow trench isolation structure.