A structure of a trench capacitor and method for manufacturing the same. The method includes providing a substrate having a defined memory area and logic area, and performing an STI process to form at least one STI region on the memory area of the substrate and at least one STI region on the logic area of the substrate. Then, a patterned mask is formed on the substrate and the STI region to partially expose the STI region and partially expose the substrate surrounding the STI region. Next, the STI region and the substrate not covered by the mask are etched to from a plurality of deep trench.