Plant diseases caused by plant viruses and pathogens seriously affect the production and storage of food crops. With the emergence of drug resistance, it is very difficult to control. Natural products are the source of new drug discovery. Here, the natural product streptindole was found to have good antiviral activity against tobacco mosaic virus (TMV) and fungicidal activities against 14 kinds of phytopathogenic fungi. A series of derivatives of streptindole were designed, synthesized, and evaluated for their antiviral and fungicidal activities. Compounds 4, 5, 11, 12c, 12d, 13d, and 13i–13l showed higher anti-TMV activities than ribavirin (inhibitory rate: 38, 37, and 40% at 500 μg/mL for inactivation, curative, and protection activity in vivo, respectively), among which compound 12d (inhibitory rate: 57, 55, and 53% at 500 μg/mL for inactivation, curative, and protection activity in vivo, respectively) with excellent antiviral activity was further evaluated for the mode of action. The mechanism research revealed that 12d can break the three-dimensional structure of TMV coat protein (CP) through hydrogen bonds, thus inhibiting the assembly of virus particles. The molecular docking result showed that compound 12d did exhibit strong interaction with TMV CP. The derivatives of streptindole also displayed broad-spectrum fungicidal activities. The current study provided valuable insights into the antiviral and fungicidal activities of streptindole derivatives.