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Foliar application of selenium (Se) fertilizer has been widely used in the production of Se-rich rice. However, the effect of Se-nanoparticles (SeNPs) fertilizer on rice quality remains largely unknown. Two bioSeNPs fertilizers were applied at different Se concentrations to explore the effect of the foliar application of SeNPs fertilizer on various rice grain qualities. The results showed that Se treatments resulted in 1.93–9.09 and 1.89–7.73 folds of total Se contents in brown and polished rice relative to the CK, respectively. Moreover, the Se treatments led to 1.04–2.33 folds increases in Cd contents, 14.6–26.4% decreases in As contents, a 13.9–16.7% reduction in Cr contents and no changes in Pb contents to that of the CK in rice grains. In addition, SeNPs exhibited no obvious impact on rice eating and cooking quality, and only the XY1 treatment could slightly improve the fatty acid content. Interestingly, Se treatments enhanced the contents of more than half of volatile organic compounds in brown rice. In general, SeNPs fertilizer XY at 6.4 g/ha was identified as the optimum choice for improvement in grain Se contents and grain qualities.