To find good antifungal substances by the bioactivity-guided isolation method, we tracked down the effective antifungal substances in the bark and leaves of Zanthoxylum avicennae, and isolated three antifungal compounds 1, 2, and 3. The structures were identified as xanthyletin, luvangetin, and avicennin by 1H-NMR, 13C-NMR, and HRMS spectra. Particularly, compound 2 had several isomers, and the 1H-NMR spectra of 2 in different solvents showed a significant difference. To determine the stereo structure of 2, a single crystal was prepared and identified by X-ray diffraction as Luvangetin. Moreover, the difference of 1H-NMR data of 2 between in solvent dimethyl sulfoxide-d6 (DMSO-d6) and deuterated chloroform (CDCl3), and other reported isomers were discussed for the first time. The bioassay results indicated that the three compounds 1, 2, and 3 displayed low to high antifungal activities against tested phytopathogenic fungi. In particular, all compounds 1, 2, and 3 showed excellent antifungal activities against Pyricularia oryzae and Z. avicennae, with the values of half maximal effective concentration (EC50) ranging from 31 to 61 mg/L, and compound 3 was also identified as a more potent inhibitor against Fusaium graminearum (EC50 = 43.26 ± 1.76 mg/L) compared with fungicide PCA (phenazine-1-carboxylic acid) (EC50 = 52.34 ± 1.53 mg/L). The results revealed that compounds 1, 2, and 3 were the main antifungal substances of Z. avicennae, and can be used as lead compounds of a fungicide, which has good development value and prospect.