A method of fabricating trench capacitors is provided. A plurality of trenches is formed in the substrate by performing a patterning process with a patterned mask layer on a substrate. A bottom electrode is formed in the substrate of the surface of the trench. A portion of the patterned mask layer is removed so as to expose a portion of the substrate at two sides of the top of the trench. A capacitor dielectric layer is formed on the substrate and the surface of the trench. A conductive layer is formed over the substrate. The conductive layer is at least filled into the trench and covers the capacitor dielectric layer. The patterned mask layer and a portion of the conductive layer are removed and the portion of the conductive layer which covers the capacitor dielectric layer is reserved as to form a top electrode.