A manufacturing method of a capacitor structure is provided, which includes the steps of: on a substrate having a first oxide layer, (a) forming a first suspension layer on the first oxide layer; (b) forming a first shallow trench into the first oxide layer above the substrate; (c) forming a second oxide layer filling the first shallow trench; (d) forming a second suspension layer on the second oxide layer; (e) forming a second shallow trench through the second suspension layer into the second oxide layer above the first suspension layer; (f) forming at least one deep trench on the bottom surface of the second shallow trench through the second and the first oxide layers, (g) forming an electrode layer on the inner surface of the deep trench; and (h) removing the first and second oxide layers through the trench openings in the first and the second suspension layers.