Cadmium (Cd) accumulation in rice (Oryza sativa L.) and its potential risks for human health have attracted great attention. Several Cd-resistant bacteria can promote plant growth and alleviate Cd toxicity to rice, but how they regulate Cd2+ flux in rice roots is still poorly understood. Here, a new Cd-resistant endophytic bacterium Ralstonia sp. YDR was isolated and used to evaluate its role in reducing rice Cd accumulation. Ralstonia sp. YDR tolerated 80 mg L−1 Cd and removed amounts of Cd via bio-adsorption and bio-absorption. Ralstonia sp. YDR also harbored good alkalizing ability and exhibited typical plant growth-promoting characteristics. Hydroponic experiment showed that inoculation with Ralstonia sp. YDR not only significantly promoted rice growth but also decreased rice Cd by 14.4–41.3%. Further analyses verified the involvement of Ralstonia sp. YDR in increasing the activities of catalase, glutathione, peroxidase, and superoxide dismutase by 27.7–77.3%, 1.7–57.6%, 57.4–100.8%, and 5.31–60.2%, and decreasing the activity of malonaldehyde by up to 56% in rice seedlings as compared with control. Moreover, a significant reduction in Cd2+ influx and H+ efflux occurred in rice roots after inoculating with Ralstonia sp. YDR. Collectively, bacterial adsorption and absorption of Cd, bacteria-aided antioxidation, and bacterial regulation of Cd2+ and H+ fluxes all contributed to a low Cd accumulation in rice. Our study provides new clues to better understand microbial mechanisms underlying the low Cd accumulation in rice plants, which helps to enhance the production of low Cd rice in agricultural practice.