AbstractBackgroundNatural products are important sources of biopesticides to control plant virus, and flavonoids are identified as promising anti‐tobacco mosaic virus (TMV) agents. Since Desmodium caudatum is a rich source of flavonoids, this study focuses on the discovery of the new anti‐TMV active flavonoids from D. caudatum and their possible mode of action.ResultsThree new (compounds 1–3) and nine known (compounds 4–12) C‐alkylated flavonoids were isolated from D. caudatum. To the best of our knowledge, the framework of 1–3 was reported in natural products for the first time. In addition, 1–3, 5, and 6 showed notable anti‐TMV activity with inhibition rates in the range of 35.8–64.3% at a concentration of 50 μg/mL, and these rates are higher than that of positive control (with inhibition rates of 34.6% ± 2.8). In addition, the structure–activity relationship study revealed that the (pyrrol‐2‐yl)methyl moiety on flavone can significantly increases the activity. This result is helpful to find new anti‐TMV inhibitors.ConclusionC‐Alkylated flavonoids showed potent activities against TMV with multiple modes of actions. The increase of defense‐related enzyme activities, up‐regulate the expression of defense related genes, down‐regulate the expression of Hsp70 protein by inhibiting the related Hsp genes that are involved in tobacco resistance to TMV. By the actions mentioned earlier, the infection of TMV was influenced, thereby achieving the effects of control of TMV. The successful isolation of the earlier‐mentioned flavonoids provide the new source of biopesticides to TMV proliferation, and also contribute to the utilization of D. caudatum. © 2023 Society of Chemical Industry.