Prochloraz is an extensively used imidazole fungicide in agriculture, but low water solubility limits its application. In the present study, inclusion complex nanofibers of prochloraz and Hydroxypropyl-γ-Cyclodextrin (prochloraz/HPγCD-IC-NF) were prepared by electrospinning method. The results of various characterization experiments indicated that prochloraz was effectively encapsulated in the cyclodextrin cavity to form inclusion complex nanofibers. Phase solubility study demonstrated that HPγCD had a significant solubilization effect on prochloraz. In 10 mM HPγCD solution, the solubility of prochloraz was increased about 2.68 times. Thermogravimetric analysis experiments indicated the beginning thermos-decomposed temperature of prochloraz in prochloraz/HPγCD-IC-NF was raised by 31℃ (from 281℃ to 312℃). The molecular simulation visually showed the best state and the most stable model of prochloraz entering the cyclodextrin cavity. In addition, the fungal inhibitory activity of prochloraz/HPγCD-IC-NF against Gibberella was 4.559 times to that of prochloraz. In conclusion, the preparation of inclusion nanofibers can improve the water solubility, thermal stability and antifungal activity of mimosine, which has the potential to reduce environmental damage in agricultural applications.