A method of manufacturing a deep trench capacitor. A first silicon oxide layer is formed on a substrate. A first trench is formed in the substrate. A rugged polysilicon layer is formed on the surface of the first trench. The grains of the rugged polysilicon layer are distributed discretely on surface of the first trench. A second silicon oxide layer is formed on the rugged polysilicon layer. The exposed substrate in the first trench is etched, in order to form a plurality of second trenches in the substrate of the first trench. The first and second silicon oxide layer are removed. A first conductive layer is formed over the substrate and conformal to the first trench and the second trenches. A dielectric layer is formed on the first conductive layer. A second conductive layer is formed on the dielectric layer.