Difenoconazole (DIF) is a representative variety of broad-spectrum triazole fungicides and liposoluble pesticides. However, the water solubility of DIF is so poor that its application is limited in plant protection. In addition, the conventional formulations of DIF always contain abundant organic solvents, which may cause pollution of the environment. In this study, two DIF/cyclodextrins (CDs) inclusion complexes (ICs) were successfully prepared, which were DIF/β-CD IC and DIF/hydroxypropyl-β-CD IC (DIF/HP-β-CD IC). The effect of cyclodextrins on the water solubility and the antifungal effect of liposoluble DIF pesticide were investigated. According to the phase solubility test, the molar ratio and apparent stability constant of ICs were obtained. Fourier transform infrared spectroscopy, thermal gravity analysis, X-ray diffraction and scanning electron microscopy were used systematically to characterize the formation and characteristics of ICs. The results noted that DIF successfully entered the cavities of two CDs. In addition, the antifungal effect test proved the better performance of DIF/HP-β-CD IC, which exceeded that of DIF emulsifiable concentrate. Therefore, our study provides informative direction for the intelligent use of liposoluble pesticides with cyclodextrins to develop water-based environmentally friendly formulations.