A manufacturing method of a contact structure includes the following steps. A substrate is provided, and the substrate includes a first region and a second region. A dielectric layer is formed on the substrate. A photoresist layer is formed on the dielectric layer. An exposure process is performed. The exposure process includes first exposure steps and second exposure steps. Each of the first exposure steps is performed to a part of the first region of the substrate. Each of the second exposure steps is performed to a part of the second region of the substrate. Each of the second exposure steps is performed with a first overlay shift by a first predetermined distance. A develop process is performed for forming openings in the photoresist layer.