Memory cells with vertical transistor and capacitor and fabrication methods thereof. The memory cell comprises a substrate with a trench. A capacitor is disposed at the bottom of the trench. A first conductive layer is electrically coupled to the capacitor. The first conductive layer is isolated the substrate by a collar dielectric layer. A trench top oxide (TTO) layer is disposed on the first conductive layer. A vertical transistor is disposed over the TTO layer. The vertical transistor comprises a gate dielectric layer disposed on the sidewalls of the upper portion of the trench, and a metal gate disposed in the upper portion of the trench.