The invention relates to a semiconductor device and a manufacturing method thereof. The semiconductor device comprises a gate structure, germanium containing semiconductor layers and a doped epitaxial semiconductor layer, wherein the gate structure is positioned on a substrate; the germanium containing semiconductor layers are positioned on two sides of the gate structure; the doped epitaxial semiconductor layer epitaxially grows between the germanium containing semiconductor layers; and bottom surfaces of the germanium containing semiconductor layers and the epitaxial semiconductor layer are positioned on the same horizontal plane, wherein the epitaxial semiconductor layer is used as a channel region; and the germanium containing semiconductor layers are used as source and drain extension regions; according to the invention, shallow junction depths (or small thickness) and high doping concentration of the source and drain extension regions can be advantageously achieved.