A method for manufacturing a semiconductor structure includes the following steps. First, a semiconductor substrate is provided and a patterned pad layer is formed on the semiconductor substrate so as to expose a portion of the semiconductor substrate. Then, the semiconductor substrate exposed from the patterned pad layer is etched away to form a trench inside the semiconductor substrate. A selectively-grown material layer is selectively formed on the surface of the trench, followed by filling a dielectric precursor material into the trench. Finally, a transformation process is carried out to concurrently transform the dielectric precursor material into a dielectric material and transform the selectively-grown material layer into an oxygen-containing amorphous material layer.