The invention discloses a method for overcoming incompatibility of distant hybridization stigmas of plants. According to the method, a pollination area of the stigmas is irradiated by using laser, the intensity and irradiation time of the laser are controlled, the pollination area of the stigmas is not destroyed completely, the identification of the stigmas on pollen specificity is reduced, so that the fertilization of ovules of paeonia lactiflora is completed, the problem of affinity between peony pollen and paeonia lactiflora stigmas is effectively solved, the fertilization process is normally completed, fusion of different genetic resources is effectively promoted, the genetic diversity of germplasm resources is further enriched, and a foundation is laid for further breeding of excellent new peony varieties. Meanwhile, the method can also be explored and applied to distant hybridization work of other plants with stigma incompatibility.