Provided is a capacitor structure including a substrate, a dielectric layer, a first conductive layer, and a cup-shaped capacitor. The dielectric layer is located on the substrate. The first conductive layer is located in the dielectric layer. The cup-shaped capacitor penetrates through the first conductive layer and is located in the dielectric layer. The cup-shaped capacitor includes a bottom electrode, a capacitor dielectric layer, and a top electrode. Two sidewalls of the bottom electrode are electrically connected to the first conductive layer. The capacitor dielectric layer covers a surface of the bottom electrode. The top electrode covers a surface of the capacitor dielectric layer. The capacitor dielectric layer is located between the top electrode and the bottom electrode. A top surface of the bottom electrode is lower than a top surface of the top electrode. Also the invention provides a method of manufacturing the capacitor structure.