Methods for manufacturing MEMS structures are provided. The method for manufacturing a microelectromechanical system (MEMS) structure includes etching a MEMS substrate to form a first trench and a second trench and etching the MEMS substrate through the first trench and the second trench to form a first through hole and an extended second trench. The method for manufacturing a MEMS structure further includes etching the MEMS substrate through the extended second trench to form a second through hole. In addition, 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 height of the MEMS substrate.