A method for fabricating a semiconductor device is described. The method includes providing a substrate having a trench therein, and a trench device in the trench. The trench device includes two gate structures disposed on the sidewalls of the trench, a doped region in the substrate between the gate structures and an inter-gate dielectric layer disposed on the surface of the gate structures. A thermal treatment process in a nitrogen-containing ambient is performed to remove the native oxide layer formed on the surface of the doped region. Then, a conductive layer is formed to fill in the trench.