The present disclosure provides a semiconductor structure and a manufacturing method thereof. The manufacturing method of the semiconductor structure includes: forming a first patterned mask layer on an upper surface of a first filling dielectric layer, the first patterned mask layer including a plurality of pattern units; etching the first filling dielectric layer based on the first patterned mask layer to form etched recesses; forming a second filling dielectric layer, the second filling dielectric layer filling up the etched recesses and covering the first patterned mask layer; removing the first patterned mask layer, and parts of the second filling dielectric layer on the first patterned mask layer and between the pattern units; removing the remaining first filling dielectric layer to form a plurality of capacitor contact holes exposing the substrate; and forming, in the capacitor contact holes, capacitor contact structures located on the two opposite sides of the BLs.