The present invention discloses a method for site-directed modification of whole plant through gene transient expression. The method as provided for conducting site-directed modification to a target fragment of a target gene in a whole plant comprises the following steps: transiently expressing a sequence-specific nuclease in said plant, wherein a whole plant is used as the subject for transient expression, said sequence-specific nuclease targets and cleaves said target fragment, thereby the site-directed modification is achieved via the self DNA repairing of said plant. In the present invention, tissue culture is omitted by transient expression of the sequence-specific nuclease; mutation is obtained at whole plant level; the method is independent of the genotype and recipient, and thus can be applied to various varieties of various species; T1 mutants can be obtained directly and the mutation can be stable inherited; more importantly, the mutant plant as obtained is free of exogenous genes, and thus have higher bio-safety.