A transistor device structure includes a substrate, a first transistor layer and a second transistor layer. The second transistor layer is disposed between the substrate and the first transistor layer. The first transistor layer includes an insulating structure and a first transistor unit. The insulating structure is disposed on the second transistor layer and has a protruding portion. The first transistor unit includes a gate structure, a source/drain structure, an embedded source/drain structure and a channel. The source/drain structure is disposed beside the gate structure and over the insulating structure. The embedded source/drain structure is disposed underneath the source/drain structure and in the insulating structure. The channel is defined between the protruding portion and the gate structure.