A method for generating masks for manufacturing of a semiconductor structure includes the following steps. First, a design pattern is provided to a processor. The design pattern includes at least one first pattern and at least two second patterns shorter than the first pattern, wherein two of the second patterns are arranged in a line along an extending direction of the patterns. Then, the second patterns are elongated by the processor such that the two second patterns arranged in the line are separated from each other by a distance equal to a minimum space of the design pattern. The design pattern is divided into a first set of patterns and a second set of patterns by the processor. A first mask is generated by the processor based on the first set of patterns. A second mask is generated by the processor based on the second set of patterns.