A method for forming a semiconductor structure includes the steps of providing a substrate having a device region and an alignment mark region, forming a first dielectric layer on the substrate and a second dielectric layer on the first dielectric layer, forming a conductive via in the second dielectric layer on the device region, forming a mask layer on the second dielectric layer, etching the second dielectric layer and the first dielectric layer through an opening of the mask layer on the alignment mark region to form a first trench through the second dielectric layer and an upper portion of the first dielectric layer and a plurality of second trenches in the first dielectric layer directly under the first trench. Afterward, a memory stack structure is formed on the second dielectric layer, covering the conductive via and filling into the first trench and the second trenches.