The invention discloses a method for evaluating the unexpected effect of genetically modified stress-resistant wheat with a GmDREB1 gene and provides a method for evaluating whether a genetically modified plant with the GmDREB1 gene has the unexpected effect or not. Experimental results show that compared with a reported receiver plant jimai19, the selected stress-resistant genetically modified wheat T349 with the GmDREB1 gene has high drought resistance and salt resistance and has broader application prospect in production; the research applies an RNA-seq method to evaluate the unexpected effect of the genetically modified wheat, and important data support is provided for discussion of the method for evaluating the unexpected effect of the genetically modified stress-resistant wheat with the GmDREB1 gene and industrialization of genetically modified stress-resistant wheat.