Embodiments of the present invention are directed to an improved method for forming dual oxide layers at the bottom of a trench of a substrate. A substrate has a trench which includes a bottom and a sidewall. The trench may be created by forming a mask oxide layer on the substrate; defining the mask oxide layer to form a patterned mask oxide layer and exposing a partial surface of the substrate to form a window; and using the patterned mask oxide layer as an etching mask to form the trench in the window. A first oxide layer is formed on the sidewall and the bottom of the trench of the substrate. A photoresist layer is formed on the substrate, filling the trench of the substrate. The method further comprises partially etching back the photoresist layer to leave a remaining photoresist layer in the trench. The height of the remaining photoresist layer is lower than the depth of the trench. A curing treatment of the remaining photoresist layer is performed after the partial etching. The patterned mask oxide layer and a portion of the first oxide layer are removed to leave a remaining first oxide layer at the bottom of the trench. The remaining photoresist layer is removed. A second oxide layer is formed on the substrate covering at least the remaining first oxide layer to form the dual oxide layers at the bottom of the trench.