A method of applying a non-genetic substance to perform site-directed reform of a plant genome. The method comprises the following steps: introducing a non-genetic substance into a cell or a tissue or a plant part of a target plant, the non-genetic substance being a nuclease specific to a target segment or an mRNA expressing the nuclease, the nuclease being a TALEN nuclease, a zinc finger nuclease (ZFN), clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) nuclease, or all nucleases capable of realizing genome editing. The nuclease acts to cut the target segment, and then site-directed reform of the target segment is completed via a DNA repair of the plant.
