The present invention discloses a mask set for compensating for a misalignment between the patterns and method of compensating for a misalignment between the patterns. A mask set of the present invention comprises a first mask consisted of a mask substrate on which a main pattern and a plurality of sub-patterns are formed, said sub-patterns formed at a side of the main pattern; a second mask consisted of a mask substrate on which a plurality of hole patterns are formed, the hole patterns corresponded to spaces between the main pattern and the sub-patterns of the first mask, respectively when the first and second mask are overlapped to each other; and a third mask consisted of mask substrate on which a plurality of bar patterns are formed, the bar patterns corresponded to the hole patterns of the second mask, respectively when the second and third mask are overlapped to each other.