An alignment method of mask patterns includes forming a first layer by transferring a first mask pattern onto a wafer, forming a second layer by transferring a second mask pattern onto the first layer, and particularly a first alignment step, forming the first layer, which performs alignment for minimizing offset between a center position of the wafer and a center position of the first mask pattern and a residual rotation error between the wafer and the first mask pattern and additional alignment for compensating an amount of possible deviation of superposition of the second layer pattern on the first layer pattern, and a second alignment step, forming the second layer, which performs only alignment for minimizing offset between a center position of the first layer pattern and a center position of the second mask pattern and a residual rotation error between the first layer pattern and the second mask pattern.