Semiconductor structures and method for manufacturing the same are provided. The method for manufacturing the semiconductor structure includes forming a first fin structure including first semiconductor material layers and second semiconductor material layers alternately stacked over a substrate and forming an isolation structure surrounding the first fin structure. The method for manufacturing the semiconductor structure also includes forming a first capping layer over the isolation structure and covering a top surface and sidewalls of the first fin structure and etching the isolation structure to form a first gap between the first capping layer and a top surface of the isolation structure. The method for manufacturing the semiconductor structure also includes forming a protection layer covering a sidewall of the first capping layer and filling in the first gap.