A semiconductor structure and a manufacturing method thereof are provided. The manufacturing method includes: providing a substrate; forming an ion implantation area in the substrate, an upper surface of the ion implantation area having a distance from an upper surface of the substrate; forming an initial word line trench in the substrate, the initial word line trench extending from the upper surface of the substrate into the ion implantation area; widening the initial word line trench to form a word line trench, a width of a bottom of the word line trench being greater than a minimum width of the word line trench.