The invention relates to a manufacturing method of a semiconductor structure. The method includes the following steps that: a substrate and discrete fins on the substrate are provided, the extending direction of the fins is a first direction, and a direction perpendicular to the first direction is a second direction; an initial isolation layer between the fins is formed on the substrate and includes a first initial isolation layer for achieving the isolation of the fins in the first direction; part of the first initial isolation layer is removed by a certain thickness, so that a first isolation layer is formed, and the top of the first isolation layer is lower than the tops of the fins, and a trench is formed between the fins; a second isolation layer filling the trench is formed; protective sidewalls are formed on the sidewalls of the second isolation layer which are higher than the tops of the fins; and part of a second initial isolation layer and the second isolation layer are removed by a certain thickness. According to the manufacturing method of the semiconductor structure of the invention, the protective sidewalls are formed on the sidewalls of the second isolation layer which are higher than the tops of the fins, and therefore, when part of the second isolation layer is removed by a certain thickness, the protective sidewalls can protect the sidewalls of the second isolation layer, and therefore, the problem of the formation of protrusion defects of the second isolation layer because of insufficient lateral etching can be avoided.