The present disclosure provides a method for preparing a semiconductor structure. The method includes the following steps. A mask stack including a first mask and a second mask is formed on a substrate. A plurality of third masks are formed. A patterned layer including first openings is formed. Portions of the second mask are removed through the first openings and the third masks to form second openings, and portions of the first mask are exposed through the second openings. A plurality of self-aligned protecting structures are formed in the second openings. Portions of the second mask exposed through the third masks are removed to form third openings, and portions of the first mask are exposed through the third openings. The portions of the first mask are removed to form a hybrid hard mask. The substrate is etched through the hybrid hard mask to form a plurality of recesses.