The invention relates to a preparation method of a high-voltage super-junction structure. The preparation method comprises the following steps of 1, performing trench etching on a semiconductor substrate to obtain a wide groove; 2, performing deposition of a second conductive type epitaxial layer above the wide groove to obtain the second conductive type epitaxial layer; 3, performing deposition of a first conductive type epitaxial layer above the wide groove to obtain the first conductive type epitaxial layer; 4, repeatedly executing the deposition process steps of the second conductive typeepitaxial layer and the first conductive type epitaxial layer until the wide groove is fully filled; and 5, performing thinning on the front surface and the back surface of the semiconductor substrateto obtain the super-junction structure with alternately arranged second conductive type column and first conductive type column. The process steps are simple and compatible with the existing process;and by adopting a common etching process with relatively low depth-to-width ratio, silicon columns with higher depth-to-width ratio are formed, so that extra photoetching and injection are not needed, thereby lowering cost.