A method for filling gaps of semiconductor device and a semiconductor device with insulation gaps formed by the same are provided. First, a silicon substrate with plural protruding portions is provided, and the protruding portions are spaced apart from each other by gaps with predetermined depths. A nitride-containing layer is formed above the silicon substrate for covering the protruding portions and surfaces of the gaps as a liner nitride. Then, an amorphous silicon layer is formed on the nitride-containing layer. An insulating layer is formed on the amorphous silicon layer, and the gaps are filled up with the insulating layer.