A semiconductor device with embedded cell is provided. A silicon substrate has a first area with at least one first cell and a second area with at least one second cell. The first cell is positioned in the first area and formed in a trench of the silicon substrate, and the second cell is positioned in the second area and formed on the silicon substrate. The first cell includes a first dielectric layer formed on sidewalls and a bottom of the trench, a floating gate formed on the first dielectric layer and embedded in the trench, a second dielectric layer formed on the floating gate and embedded in the trench, and a control gate formed on the second dielectric layer and embedded in the trench, wherein the control gate is separated from the floating gate by the second dielectric layer.