A multi bits flash memory device and a method of operating the same are disclosed. The multi bits flash memory device includes: a stacked structure including: a first active layer with a mesa-like form disposed on a substrate; a second active layer, having a different conductivity type from the first active layer, formed on the first active layer; an active interlayer isolation layer interposed between the first active layer and the second active layer such that the first active layer is electrically isolated from the second active layer; a common source and a common drain formed on a pair of opposite side surfaces of the stacked structure; a common first gate and a common second gate formed on the other pair of opposite side surfaces of the stacked structure; a tunnel dielectric layer interposed between the first and second gates and the first and second active layers; and a charge trap layer, storing charges that tunnel through the tunnel dielectric layer, interposed between the tunnel dielectric layer and the first and second gates.