Autophagy is a highly conserved pathway that mediates bulk degradation of cellular components in lysosomes/vacuoles and plays an important role in filamentous fungi by impacting growth, morphology and development. However, in leaf rust, the role of autophagy is poorly understood. In this study, we identified the structure of autophagy in leaf rust infection structures by using transmission electron microscopy (TEM). The results suggest that autophagy can be strongly induced in the haustorium mother cell (HMC) but did not occur in other special infection structures, such as the appressorium, substomatal vesicle and haustorial. Applying the autophagy inhibitor 3-mehyladenine (3-MA) to leaf rust resulted in significant arrest of mycelial growth and delays in leaf rust infection. These results suggest that autophagy can be induced in HMC and is important for fungal infection of wheat. This research will help us to expand our understanding of the physiological functions of autophagy in filamentous fungi.