A method of manufacturing a semiconductor structure includes the following operations. A substrate embedded with a shallow trench isolation is received. A first dielectric layer is formed on the substrate. An etching process is performed to form a hole in the first dielectric layer and form a pit in the substrate, wherein an upper surface of the shallow trench isolation is exposed from the hole, and the pit is adjacent to the shallow trench isolation. A second dielectric layer is formed on the first dielectric layer and the shallow trench isolation and in the pit. The second dielectric layer is treated with a plasma to convert a first portion of the second dielectric layer substantially on the first dielectric layer and the shallow trench isolation to a plasma-treated layer. The plasma-treated layer is removed to remain a second portion of the second dielectric layer in the pit.