Vegetable crops such as tomato are highly susceptible to various pathogens. Nanoparticles (NPs) are emerging as effective nano-bactericides for managing plant pathogens. Communities of rhizosphere bacteria are essential for plant physiological health and also serve as a critical factor in evaluating the environmental compatibility of NPs. We evaluated the effects of a nano-bactericide (Cu-Ag nanoparticles) and a commercial bactericide (thiodiazole-copper) on the rhizosphere microbiome of tomato. The results show that low and high doses of the two bactericides induced alterations in the bacterial community structure to differing extents. Cu-Ag nanoparticles increased the relative abundance of potentially beneficial bacteria, including , , , and Functional prediction revealed that Cu-Ag nanoparticles may affect the metabolic pathways of tomato root rhizosphere microorganisms and regulate the lacI/galR family, which controls virulence factors and bacterial metabolism. This study provides insight into the influence of metal nanoparticles on plant rhizosphere microbiomes and may lay a foundation for the application of nano-bactericides for the environmentally friendly control of plant diseases.