Provided is a method of manufacturing a silicon on insulator (SOI) substrate, which includes the steps of (a) forming a buried oxidation layer to a predetermined depth of a first wafer and forming an oxidation layer on a surface of the first wafer; (b) bonding a second wafer onto the first wafer; (c) selectively removing the oxidation layer so as to expose a bottom surface of the first wafer; (d) selectively removing the exposed bottom silicon layer of the first wafer using the buried oxidation layer as an etch stop layer; and (e) removing the buried oxidation layer to expose a top surface of the first wafer, and thinning the exposed top surface of the first wafer to a predetermined thickness, so that a process can be relatively simple and can be readily carried out, thereby manufacturing an SOI substrate having a uniform silicon thickness of high quality and an ultra thin characteristic.