To elucidate the mitigation mechanisms of silicon (Si), selenium (Se), and their interaction on rice seedlings under chromium (Cr) stress, a pot soil culture experiment was conducted. The experiment used a treatment without applying Cr, Si, and Se as the control (CK). Under Cr stress (30 mg/kg), single treatments of Si and Se as well as a combined treatment were set up to thoroughly investigate the effects of Si and Se on the physiological and biochemical characteristics, element absorption, and Cr subcellular distribution in rice under Cr stress. The results showed that, compared with CK, the biomass, photosynthetic pigment content, soluble osmotic substance content, and mineral element (N, P, K, Ca, Mg, Si, Se) content of rice seedlings decreased under Cr stress. In contrast, the activities of antioxidant enzymes (GR, SOD, CAT, POD), the contents of reactive oxygen species (MDA, H₂O₂), and the contents of redox substances (GSH, Pro) significantly increased. Under Cr stress, the application of either Se or Si could improve the aforementioned indicators, and the Se treatment exhibited a better effect than the Si treatment. Additionally, the application of Si and Se also reduced the Cr content in rice plants and altered the subcellular distribution ratio of Cr in rice roots. Specifically, it increased the distribution ratio of Cr in the cell wall and decreased the distribution ratios of Cr in the cell membrane, organelles, and cytoplasm. Moreover, the effect of Si was superior to that of Se in this regard. In summary, under Cr stress, Se demonstrated more prominent performance in improving plant physiological and biochemical characteristics and promoting mineral element absorption, while Si showed a better effect in inhibiting Cr uptake. The two elements exhibited a synergistic effect, resulting in a significant 72.18% reduction in plant Cr content compared to the treatment under Cr stress without applying Si and Se.