There are provided a semiconductor device having a structure which can realize not only suppression of a punch-through current but also reuse of a silicon wafer used for bonding, in manufacturing a semiconductor device using an SOI technique, and a manufacturing method thereof. A semiconductor film into which an impurity imparting a conductivity type opposite to that of a source region and a drain region is implanted is formed over a substrate, and a single crystal semiconductor film is bonded to the semiconductor film by an SOI technique to form a stacked semiconductor film. A channel formation region is formed using the stacked semiconductor film, thereby suppressing a punch-through current in a semiconductor device.