The increasing cadmium (Cd) levels in agricultural soils have become a worldwide concern for food crop security. Cd accumulation in the soil-plant system is closely related to other coexisting factors. In this study, the effects of different levels of Zn or Ni on Cd accumulation in tomato plants and on the rhizosphere soil bacterial community structure were analyzed by coupling pot experiments with high-throughput sequencing. The results demonstrated that tomato plants (Lycopersicon esculentum) in Zn-Cd and Ni-Cd co-contaminated soils exhibited lower relative growth rates. Co-contamination at low levels tended to reduce the bioaccumulation of heavy metals in the roots of plants, whereas increased contaminant concentrations produced the opposite effect. In the presence of 200 mg/kg Zn or 20 mg/kg Ni, the biomass of plant roots increased by 4.95−23.16% and the Cd content of the plant roots decreased by 17.36−68.93% due to the antagonistic effects between Cd and Zn/Ni. In addition, the richness and diversity of the bacterial community were significantly altered under HMs co-contamination, and the number of special bacteria was positively correlated with the level of heavy metals in the rhizosphere soil. The relative abundance of Proteobacteria increased and that of Actinobacteria decreased in soils with low levels of heavy metals. This may improve the tolerance of plant roots to heavy metals and reduce the accumulation of Cd in plant roots. These findings highlight the important role of coexisting elements in the inhibition of Cd accumulation in tomatoes and offer important information for the production of safe crops.