A method of filling a trench comprises heating a semiconductor substrate having a trench formed therein and an oxide film formed at least on the sidewall of the trench and supplying an aminosilane gas to the surface of the substrate so as to form a seed layer on the semiconductor substrate, heating the semiconductor substrate having the seed layer formed thereon and supplying a monosilane gas to the surface of the seed layer so as to form a silicon film on the seed layer, filling the trench of the semiconductor substrate, which has the silicon film formed thereon, with a filling material that shrinks by burning, and burning the semiconductor substrate coated by the filling material filling the trench in an atmosphere containing water and/or a hydroxy group while changing the filling material into a silicon oxide and changing the silicon film and the seed layer into a silicon oxide.