Methods for manufacturing MEMS structures are provided. The method includes forming a first trench and a second trench in a MEMS substrate by performing a main etching process and etching the MEMS substrate through the first trench and the second trench to form a first through hole and an extended second trench by performing a first step of an over-etching process. The method further includes etching the MEMS substrate through the extended second trench to form a second through hole by performing a second step of the over-etching process. In addition, a width of the first trench is greater than a width of the second trench, and a height of the first trench is greater than ¾ of a height of the MEMS substrate, and a height of the second trench is smaller than ⅔ of the MEMS substrate.