A semiconductor device in which a channel region of MOS transistor is provided not to include a non-flat active region end portion and a manufacturing method thereof is disclosed. According to one aspect, there is provided a semiconductor device comprising a semiconductor substrate, a device isolation separating active region, wherein at least a portion of the device isolation is provided in the semiconductor substrate, and a memory cell including a memory cell transistor that comprises a channel region separated by a slit and constituted of a flat active region alone, a charge storage layer provided on a gate dielectric on the channel region, and a first gate electrode provided on an inter-electrode dielectric so as to cover the charge storage layer, and a select transistor that comprises a second gate electrode provided on the gate dielectric on the active region and electrically connected to a wiring.