Overlay-shift measurement systems are provided. An overlay-shift measurement system includes an optical device, a first light detection device and a processor. The optical device is configured to provide an input light to a metrology target of a semiconductor structure. The first light detection device is configured to receive a transmitted light from the metrology target when the input light penetrates the metrology target. The processor is configured to determine whether overlay-shift between a plurality of first photonic crystals and a plurality of second photonic crystals in the metrology target is present according to characteristics of the transmitted light.