Abstract: Iron plaque (IP) is a colloidal membrane consisting of iron (hydr)oxides formed on the root surface of rice (Oryza sativa), which not only enhances the adaptation of roots to the surrounding waterlogging but also affects nutrient uptake by rice. However, further exploration of methods to increase the Se accumulation in rice grains by regulating IP formation on the rice root surface is needed. Experiments on rice plants with different levels of phosphate-iron ratios (P/Fe), urea peroxide (UP), and alternation of wetting and drying (AWD) treatments were conducted under pot cultivation with mildly acidic (pH = 6.1) soil conditions to investigate the effects of these three IP-controlling techniques on IP formation and Se accumulation in grains. The results indicated that the IP content on the root surface and the grain Se content after a 1∶5 P/Fe treatment were significantly higher than that after a 1∶0 P/Fe treatment. The IP content and grain Se content after 90 kg∙hm⁻² UP treatment were significantly higher than that without UP. When P/Fe was less than 1∶3 or the UP dose was greater than 60 kg∙hm⁻², the variation trend of the grain Se content became steady. In addition, the IP content and grain Se content after long-term waterlogging treatment were remarkably higher than those of the control (irrigation to maintain a shallow water layer on the soil surface before naturally drying at the grain-filling stage) and AWD treatments. Although the IP content after one cycle of AWD treatment was lower than that after long-term waterlogging, the grain Se contents were similar. Correlation analysis suggested that both amorphous and crystalline IP contents presented a significant linear correlation with the grain Se content under the P/Fe and UP treatments, whereas this phenomenon did not occur under the AWD treatment. However, the linear coefficient of the correlation between the grain Se content and crystalline IP content was higher than that between the grain Se content and amorphous IP content under the P/Fe treatment, whereas the result was the opposite in the UP treatment. In orthogonal experiments, the IP controlling techniques harvesting the highest IP formation and the most remarkable increase in the grain Se content were the treatment combination of P/Fe of 1∶1, UP of 90 kg∙hm⁻², and long-term waterlogging. The grain Se content after this treatment combination was 0.116 μg∙g⁻¹, which was 2.01 times greater than that of the control (1∶0 P/Fe, no UP application, and conventional water management). The analysis of variation indicated that the effect sequence of the three controlling techniques on the IP content and grain Se content was UP>AWD>P/Fe. The effect of the P/Fe ratio on the IP content and grain Se content under this combination treatment could be neglected. In summary, IP controlling techniques, including regulating P/Fe, applying UP, and conducting AWD treatment, can promote IP formation on the root surface and Se accumulation in roots, thereby increasing Se accumulation in rice grains. The results of this study are scientifically relevant for Se-enriched rice production.