A method for forming a semiconductor device structure is provided. The method includes forming a gate stack and a conductive layer over a semiconductor substrate. The semiconductor substrate has a first region and a second region isolated from each other by an isolation structure in the semiconductor substrate. The gate stack is formed over the first region. The method includes forming a negative photoresist layer over the first region and a first portion of the conductive layer over the isolation structure to cover the gate stack. The method includes forming a mask layer over the negative photoresist layer and the conductive layer. The mask layer has trenches over a second portion of the conductive layer. The method includes removing the second portion through the trenches. The method includes removing the mask layer. The method includes removing the negative photoresist layer.