Tilletia laevis cause common bunt and Tilletia controversa cause dwarf bunt of wheat. Both pathogens can cause fungus galls which replace with wheat grains and lead to the total loss of wheat yields. To better understand disease progression, confocal microscopy was used to construct the timeline of cell development of healthy wheat anthers, and which was approved by analyzing the expression level of some developmental and program cell death genes. Based on comparing with normal healthy anthers, tapetum cells should be disappeared at 1300 µm, but in T. laevis infected anthers, tapetum cells was visible in 2100 µm of T. controversa infected anthers. For the anthers infected by T. laevis and T. controversa, cell size and counts showed significant difference with normal anther cells. Additionally, for the anthers of five developmental stages, transcriptome profile and infected five developmental stages were also analyzed. Furthermore, we established virus-induced gene silencing (VIGS) for wheat bunt pathogens. Based on RNA-Seq data, TaEC in wheat anther were validated to contribute to the resistance to both bunt pathogens. This study firstly constructed the development timeline of wheat anthers and firstly constructed VIGS system to explore the interaction of both bunt pathogens with wheat anther development.