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Abstract Background The element selenium (Se) deficiency is thought to be a global human health problem, which could disperse by daily-supplement from Se-rich food. Increasing the accumulation of Se in rice grain is an approach matched to these nutrient demands. Nonetheless, Se is shown to be essential but also toxic to plants, with a narrow margin between deficiency and toxicity. Notably, the regulatory mechanism balancing the accumulation and tolerance of Se in Se-rich rice plants remains unknown. Results In this study, we investigated the phenotypical, physiological, and biochemical alterations of Se-rich rice in the exposure to a variety of Se applications. Results showed that the Se-rich rice was able to accumulate more abundance of Se from the root under a low Se environment comparing to the Se-free rice. Besides, excessive Se led to phytotoxic effects on Se-rich rice plants by inducing chlorosis and dwarfness, decreasing the contents of antioxidant, and exacerbating oxidative stresses. Furthermore, both phosphate transporter OsPT2 and sulfate transporters OsSultr1;2 may contribute to the uptake of selenate in rice. Conclusions Se-rich red rice is more sensitive to exogenous application of Se, while and the most effective application of Se in roots of Se-rich rice was reached in 20 μM. Our findings present a direct way to evaluate the toxic effects of Se-rich rice in the Se contaminated field. Conclusively, some long-term field trial strategies are suggested to be included in the evaluation of risks and benefits within various field managements.