A method of fabricating a memory device includes providing a substrate having a first region and a second region. A first dielectric layer is formed on the substrate in the first region. A conductive layer is formed on the substrate in the second region. A top surface of the conductive layer is lower than a top surface of the first dielectric layer. A second dielectric layer is formed on the substrate. A portion of the second dielectric layer and a portion of the conductive layer are removed to form a first opening in the conductive layer and the second dielectric layer in the second region. The first opening exposes a surface of the substrate. A portion of the substrate in the second region is removed to form a trench in the substrate in the second region. A third dielectric layer is formed in the trench and the first opening.