The invention provides a double-depth shallow channel isolation groove and a preparation method thereof. The preparation method of the double-depth shallow channel isolation groove comprises the following steps: providing a substrate, and sequentially forming a hard mask layer and a graphical first photoresist layer on the substrate; taking the graphical first photoresist layer as a mask, etchingto form a first opening and a second opening, and then removing the first photoresist layer; forming a graphical second photoresist layer on the hard mask layer; taking the graphical second photoresist layer and hard mask layer as masks, etching to form a first part of a second isolation groove, and then removing the second photoresist layer; taking the hard mask layer as a mask, and etching to form the second part and the first isolation groove of the second isolation groove so that the first isolation groove of a photosensitive region and the second isolation groove of a logic region are formed at the same time. Thus, the electrical performance of the photosensitive device is improved, the STI electrical isolation performance is also improved, the process difficulty is reduced, and the process window is expanded.