<p>Heavy metal contamination, particularly cadmium pollution, is a critical environmental concern that poses a serious threat to sustainable agriculture. Our study examined the impact of <i>Bacillus pseudomycoides</i> (Bp) on enhancing rice seedling growth, metabolism, stress tolerance, and reducing cadmium accumulation, with potential applications for mitigating heavy metal toxicity and promoting sustainable agriculture. A 50-min seed inoculation with Bp resulted in the greatest enhancements in seed emergence rate, seedling vigor, germination capability, plant stature, dry weight, and relative water content. Furthermore, inoculation with <i>B. pseudomycoides</i> enhanced cellular metabolism, growth, and stress resilience in rice seedlings, as indicated by increased levels of chlorophyll, sugars, proteins, signaling molecules (H₂O₂ and NO), and higher concentrations of zinc and iron. Antioxidant enzyme activities were also significantly elevated, particularly with the 50-min treatment, further supporting the improved stress response. Notably, this inoculation effectively reduced cadmium accumulation, demonstrating its potential for mitigating heavy metal toxicity. Molecular docking simulations suggest that <i>B. pseudomycoides</i> may inhibit key rice heavy metal transporter proteins, OsNRAMP5 and OsHMA2. These findings highlight the bacterium’s promise as a biological tool for sustainable agriculture, warranting further validation through field trials.</p>