A method of manufacturing a semiconductor structure includes providing a substrate having an active region surrounded by an isolation layer; forming a first trench and a second trench in the active region, and a third trench and a fourth trench in the isolation layer; forming a bottom work-function layer in the third trench and the fourth trench, respectively; forming a middle work-function layer on the bottom work-function layer and in the first and the second trenches; forming a top work-function layer on the middle work-function layer; and forming a capping layer on the top work-function layer that fills a remaining region of the first, the second, the third and the fourth trenches.