A semiconductor device and a manufacturing method thereof are provided. The manufacturing method includes the following steps. A core structure and a first material layer are formed on a substrate in order. A top surface of the first material layer is lower than a top surface of the core structure. A second pattern is formed on an exposed surface of the core structure. The method of forming the second pattern includes forming a second material layer on the exposed surface of the core structure and the top surface of the first material layer and performing an anisotropic etching on the second material layer. The first material layer is patterned by using the second pattern as a mask to form a first pattern. The step of forming the second material layer and the step of performing an anisotropic etching on the second material layer are performed in the same etching chamber.