A gate stack structure comprises an isolation dielectric layer formed on and embedded into a gate. A sidewall spacer covers opposite side faces of the isolation dielectric layer, and the isolation dielectric layer located on an active region is thicker than the isolation dielectric layer located on a connection region. A method for manufacturing the gate stack structure comprises removing part of the gate in thickness, the thickness of the removed part of the gate on the active region is greater than the thickness of the removed part of the gate on the connection region so as to expose opposite inner walls of the sidewall spacer; forming an isolation dielectric layer on the gate to cover the exposed inner walls. There is also provided a semiconductor device and a method for manufacturing the same. The methods can reduce the possibility of short-circuit occurring between the gate and the second contact hole and can be compatible with the dual-contact-hole process.