The invention discloses a manufacturing method of an STI structure, comprising the step of etching the hard mask, which comprises front etching and back etching; the etching parameter is changed in the back etching process to enforce side etching, so as to form a tapered cut structure at the bottom of the hard mask. In the STI structure manufactured by the method, a relatively flat angular grooveis formed at the contact of the top of the STI structure and substrate silicon, which avoids the film residues and the like formed in the following etching process; therefore the invention can be widely used for the manufacturing of semiconductor devices.