Methods for manufacturing a semiconductor structure are provided. A substrate is provided. A first lithography is performed according to a first layer mask, to form a plurality of first photonic crystals with a first pitch on a first area of a layer above the substrate. A second lithography is performed according to a second layer mask, to form a plurality of second photonic crystals with a second pitch on a second area of the layer. A light is provided to illuminate the first and second photonic crystals. Light reflected by the first and second photonic crystals or transmitted through the first and second photonic crystals is received. The received light is analyzed to detect overlay-shift between the first photonic crystals corresponding to the first layer mask and the second photonic crystals corresponding to the second layer mask.