Abstract: The sustainable development of the tobacco industry was seriously threated by tobacco viral diseases, especially for Tobacco mosaic virus (TMV) and Tobacco vein banding mosaic virus (TVBMV). Nanomaterials for nucleic acid delivery system is a green, safe, and efficient approach with great potential for the prevention and control of plant viral diseases. In this study, the optimal target sequences were screened to analyze viral inhibition of TMV and TVBMV through fusion experiment of different nanomaterials. Coat protein (CP) and P126 fragments of TMV genome sequences, CP and HC Pro fragments of TVBMV genome sequences were synthesized to dsRNA in vitro. The viral inhibition of dsRNA on TMV and TVBMV were identidied by VIGS (virus induced gene silencing) experiments. Fusion experiments between dsRNA and three types of nanomaterials, chitosan (CS), carbon quantum dots (CQD), and graphene quantum dots (GQD) were conducted to identify optimal fusion ratio. Three nanoparticle-dsRNA complexes were characterized by particle size testing instrument, Zeta potential testing instrument, and transmission electron microscope (TEM). The viral inhibition effect of three nanoparticle-dsRNA complexes were also tested. The results showed that P126 fragment of TMV and V-HC fragment of TVBMV obtained the better results by VIGS injection (average incidence inhibition rate of 53.96% and 61.22%, respectively). The results of dsRNA injection were consistent with those of VIGS injection. The dsRNA of P126 fragment had a better viral inhibition on TMV (with an average incidence inhibition rate of 58.67%), dsRNA of V-HC fragment had a better viral inhibition on TVBMV (with an average inhibition rate of 48.11%). Thus, P126 fragment and HC Pro fragment are the best targets for viral inhibition of TMV and TVBMV. The fusion experiment between dsRNA and nanomaterials indicated that the optimal fusion mass ratio of dsRNA to CS was 1∶1, and the optimal mass fusion ratio of dsRNA to CQD was 1∶10, the optimal fusion mass ratio of dsRNA and GQD was 1∶7. Nanoparticle-dsRNA complexes were characterized by particle size analysis, Zeta potential, transmission electron microscope, which proved that nanoparticle and dsRNA were successfully self-assembled. The viral inhibition experiment on TMV and TVBMV proved that nanoagents obtained significantly better viral inhibitory effect, and that CQD-dsRNA and GQD-dsRNA were the optimal nanoparticle-dsRNA complexes.