Tilletia controversa Kühn (TCK) has strong infectivity and viability and may cause great cut hazard to wheat and other crops. Composting treatment of TCK-infected wheat waste may be an effective method to eliminate the further contamination. This study applied microbial fermentation composting technique using mixed crop straws and manure to establish a bio-friendly composting method. The change of physicochemical properties of the compost was monitored regularly to detect the time course of TCK degradation and confirm the inactivation of TCK germination activity. The results of regular sampling indicate that the germination rate of TCK declines with the composting progress, and composting ten days under the condition of 50℃ to 60℃ completely inactivates the germination ability of TCK. Thus the present study provides a bio-friendly composting method for degrading TCK-infected wheat crops under TCK outbreak.