The invention provides a capacitor structure and a manufacturing method thereof. The capacitor structure comprises a first electrode plate arranged on a substrate, a first capacitor dielectric layer arranged on the first electrode plate and a second electrode plate arranged on the first capacitor dielectric layer. A part of the first electrode plate extends beyond one end of the second electrode plate to form a step. The capacitor structure also comprises an etching stop layer, an intermetallic dielectric layer, a first guide hole and a second guide hole. The etching stop layer is arranged onthe second electrode plate, and the intermetallic dielectric layer covers the etching stop layer, the second electrode plate, the first capacitor dielectric layer and the first electrode plate. The first guide hole passes through the intermetallic dielectric layer to contact the first electrode plate at the part extending beyond the second electrode plate. The second guide hole passes through theintermetallic dielectric layer and the etching stop layer to contact the second electrode plate.