A method of fabricating a trench isolation structure in a high-density semiconductor device that provides an isolation characteristic that is independent of the properties of adjacent MOS transistor devices, wherein a first trench in a first isolation area and a second trench implanted are formed on a semiconductor substrate, a nitrogen (N)-rich silicon layer is formed on the sidewall in a second isolation area, a subsequent oxidation process may be employed to fabricate oxide layers, each having a different thickness, on the sidewall surfaces of the first and second trenches. When the first and second oxide-layered trenches are filled with a stress relief liner and a dielectric material, the different thicknesses of the oxides prevent leakage currents from flowing to an adjacent semiconductor device, regardless of the doping properties of each device.