A method for fabricating semiconductor device includes the steps of: providing a substrate having a memory region and a periphery region; forming a first trench and a second trench in substrate on the memory region, wherein a width of the second trench is greater than a width of the first trench; forming a first liner in the first trench and the second trench; forming a second liner on the first liner, wherein the second liner completely fills the first trench and partly fills the second trench; and planarizing the second liner and the first liner to form a first isolation structure and a second isolation structure.