A semiconductor device structure includes a silicon-on-insulator (SOI) region. The SOI region includes a semiconductor substrate, a buried oxide layer disposed over the semiconductor substrate, and a silicon layer disposed over the buried oxide layer. The semiconductor device structure also includes a first shallow trench isolation (STI) structure penetrating through the silicon layer and the buried oxide layer and extending into the semiconductor substrate. The first STI structure includes a first liner contacting the semiconductor substrate and the silicon layer, a second liner covering the first liner and contacting the buried oxide layer, and a third liner covering the second liner. The first liner, the second liner and the third liner are made of different materials. The first STI structure also includes a first trench filling layer disposed over the third liner and separated from the second liner by the third liner.