Abstract: With the advent of transgenic plant,exogenous Bt gene utilization has offered effective opportunities for developing new series resistant crop varieties.The presence of foreign genes in transgenic plants causes physiological changes in the plants including changes of secondary metabolism,and these changes could lead to ecological effects on the environment.A train of recent research on secondary metabolite and Bt protein interactions were reviewed in this paper.The results indicate that exogenous genes rebuilding affects secondary metabolism of crops.