Based on previous research, this study synthesized 24 compounds by splicing the substructures of the indolyl group and the isothiocyanate group. Alternaria alternata, Phytophthora capsici, Botrytis cinerea, and Valsa mali were used to test the activity of the target compounds. At 100 μg/mL, compounds 8, 13, 14, and 17 exhibited excellent inhibitory effects of more than 80% on P. capsici, B. cinerea, and V. mail. The EC50 values of compounds 13 and 14 were 0.64 and 2.08 μg/mL, respectively. Potted antifungal activity demonstrated that compounds 13 and 14 had a protective effect of around 80% against B. cinerea at 200 μg/mL. Further physiological and biochemical studies on B. cinerea revealed that compound 13 thickened cell walls and caused mitochondrial vacuolization. Moreover, theoretical calculations indicated that the charge distribution of indolyl isothiocyanate compounds played a crucial role in the observed fungicidal activity. In summary, this study provided fundamental reference data for the derivative synthesis of these indolyl isothiocyanate compounds.