A method for forming a semiconductor structure includes receiving a first die having a first interconnect structure and a first bonding layer over the first interconnect structure, and a second die having a second interconnect structure and a second bonding layer over the second interconnect structure; forming a recess indenting into the first bonding layer; and forming a positioning member on the second bonding layer. The method further includes bonding the second die over the first die; and disposing the positioning member into the recess. The positioning member includes dielectric, is surrounded by the first bonding layer, and is isolated from the first interconnect structure and the second interconnect structure.