A semiconductor structure and a manufacturing method thereof are provided. The manufacturing method of the semiconductor structure comprises: providing a substrate, comprising a polysilicon layer, a first conductive layer, a first dielectric layer, a mask layer, and a sacrificial layer sequentially formed thereon, wherein the sacrificial layer has a plurality of first trenches distributed at intervals; forming a first insulating layer on the sacrificial layer; forming a protective layer, the protective layer only covering a surface of the first insulating layer above the top surface of the sacrificial layer; removing the protective layer, part of the first insulating layer, the sacrificial layer, and part of the mask layer to form a first pattern layer; and removing part of the first dielectric layer, part of the first conductive layer, and part of the polysilicon layer by using the first pattern layer as a mask to form a BL structure.