The present invention discloses a semiconductor device, comprising: a substrate, an insulating isolation layer formed on the substrate, a first active region layer and a second active region layer formed in the insulating isolation layer, characterized in that the carrier mobility of the first active region layer and/or second active region layer is higher than that of the substrate. In accordance with the semiconductor device and the manufacturing method thereof in the present invention, an active region formed of a material different from that of the substrate is used, the carrier mobility in the channel region is enhanced, thereby the device response speed is substantially improved and the device performance is enhanced greatly. Furthermore, unlike the existing STI manufacturing process, for the present invention, an STI is formed first, and then filling is performed to form an active region, thus avoiding the problem of generation of holes in STI, and improving the device reliability.