The present invention discloses a method for preparing a structure with high aspect ratio, which can be a trench or a conductor. A first mask is formed on a substrate, and a first etching process is performed to remove the substrate uncovered by the first mask to form at least one concavity. A second mask is formed on the surface of the prepared structure, a second etching process is then performed to remove the second mask on the concavity, and a third etching process is performed subsequently to extend the depth of the concavity into the substrate. To prepare a conductor with high aspect ratio in the substrate, the first mask and the second mask are preferably made of dielectric material or metal. In addition, to prepare a trench with high aspect ratio in a silicon substrate, the first mask and the second mask are preferably made of dielectric material.