Objective To optimize extraction process of tomato-derived exosomes and preliminarily exploration of the feasibility of tomato-derived exosomes as nano carriers. Methods Tomato-derived exosomes were isolated by sucrose density gradient method. Dynamic light scattering and transmission electron microscopy were used to identify the characteristics of exosomes, and MTT assay was used to detect the toxicity of exosomes in A549, A2780 and HONE1 (EBV+) cells. Tomato-derived exosomes were used to deliver model drug DiI and antisense EBV-miR-BART7-3p to prepare nanomedicines. Their cellular uptake ability was tested in three cancer cells and the silence effect of nano gene drugs was investigated by the fluorescent quantitative PCR. Results Exosomes with high yield (1.31 g/kg) were obtained by the optimized procedure. Tomato-derived exosomes exhibited nano-size and showed the spherical lipid bilayer structure, and they had no significant cytotoxicity. The nanomedicine based on exosomes could be internalized in cells and distributed in the cytoplasm. The targeted gene expression level could be effectively silenced by gene drug, and the difference was statistically significant (P < 0.05). Conclusion The extraction procedure of tomato-derived exosomes was optimized, and the feasibility of exosomes as excellent drug carriers was verified.