The present disclosure provides mark structures and fabrication methods thereof. An exemplary fabrication process includes providing a substrate having a device region, a first mark region and a second mark region; sequentially forming a device layer, a dielectric layer and a mask layer on a surface of the substrate; forming a first opening in the dielectric layer in the device region, a first mark in the dielectric layer in the first mark region, and a mark opening in dielectric layer in the second mark region, bottoms of the first opening, the first mark and the mark opening being lower than a surface of the dielectric layer, and higher than a surface of the device layer; and forming a second opening in the dielectric layer on the bottom of the first opening and a second mark in the dielectric layer on the bottom of the mark opening.