Abstract:[Objective] To clarify the mechanism of Piriformospora indica in inducing wheats against root rot. [Methods] Seeds were soaked in the suspension of P. indica, and the medium without P. indica was used as control. After Fusarium graminearum infecting wheats, this study analyzed the physiological and biochemical indexes and transcriptome changes. [Results] The pathogen F. graminearum induced the production of hydrogen peroxide in wheats, reduced the intracellular water content, and destroyed the stability of the membrane. The colonization of P. indica increased the activity of intracellular antioxidant enzymes and reduced the accumulation of oxygen free radicals in cells. Intracellular water content was further maintained, and the stability of membranes was enhanced. The colonization of P. indica also reprogrammed the mRNA transcriptome changes caused by F. graminearum. The expression of resistance-related genes was enhanced. Based on the above results, P. indica effectively improved the resistance of wheats to F. graminearum. [Conclusion] The implementation of the work will provide theoretical basis and experimental basis for in-depth understanding of plant-microbe interaction and development of new efficient and environmentally friendly root rot agents.