A capacitor structure is provided, which includes a contact layer, an insulating layer, a bottom conductive plate, a dielectric layer and a top conductive plate. The contact layer has first, second, third, fourth and fifth portions arranged from periphery to center. The insulating layer is disposed over the contact layer and has an opening exposing the contact layer. The bottom conductive plate is disposed in the opening and including first, second and third portions extending along a depth direction of the opening and separated from each other and in contact with the first, third and fifth portions of the contact layer, respectively. The dielectric layer is conformally disposed on the bottom conductive plate and in contact with the second and fourth portions of the contact layer. The top conductive plate is disposed on the dielectric layer. A method of manufacturing the capacitor is also provided.