The invention provides a manufacturing method of a semiconductor device. First, a substrate is provided. A first recess and a second recess are formed in the substrate, a width of the first recess is smaller than a width of the second recess. Then, a first spin-on dielectric (SOD) layer is formed to fill the first recess and partially fill in the second recess, and then a first processing step is performed to transfer the first SOD layer into a first silicon oxide layer, a silicon nitride layer is subsequently formed on the first silicon oxide layer in the second recess, and then a second spin-on dielectric (SOD) layer is formed on the silicon nitride layer in the second recess, and a second processing step is performed to transfer the second SOD layer into a second silicon oxide layer.