The present invention provides a capacitor structure and a manufacturing method thereof, and a semiconductor memory including the capacitor structure. The manufacturing method of the capacitor structure at least comprises the steps of: providing a semiconductor substrate comprising a peripheral area and a center area; forming a gate structure of a peripheral device at the peripheral area, and forming a first capacitor structure on the semiconductor substrate at the same time; forming a gate structure of a semiconductor memory at the center area, and forming a second capacitor structure on the first capacitor structure at the same time, wherein the second capacitor structure partly exposes the surface of the first capacitor structure; and forming a first electrode, a second electrode and a third electrode, wherein the first electrode is connected with the semiconductor substrate, the second electrode is connected with the surface of the first capacitor structure, the third electrode is connected with the surface of the second capacitor structure, the first electrode and the third electrode are conducted with each other to serve as first output ends, and the second electrode serves as a second output end. The capacitor structure of the present invention not only has large capacitance, but also has a good voltage resistant capability.