A method of fabricating a shallow trench isolation structure is disclosed. On a substrate, a pad oxide layer and a mask layer are successively formed. The pad oxide layer, the mask layer and a portion of the substrate are patterned to form a trench. After performing a rapid wet thermal process, a liner layer is formed on the exposed surface of the substrate, including the exposed silicon surface of the substrate in the trench and sidewalls and the surface of the mask layer. An oxide layer is deposited over the trench and the substrate and fills the trench. A planarization process is performed until the mask layer is exposed. The mask layer and the pad oxide layer are removed to complete the shallow trench isolation structure.