Direct discharge of untreated industrial waste water in water bodies and then irrigation from these sources has increased trace metals contamination in paddy fields of southern China. Among trace metals, cadmium (Cd) and lead (Pb) are classified as most harmful contaminants in farmland to many organisms including plants, animals and humans. Rice is a staple food which is consumed by half population of the world; due to longer growth period it can easily absorb and accumulate the trace metals from soil. The objective of study was to check the efficacy of Se and Si NPs (nanoparticles) alone or in combination on metals accumulation and Se-fortified rice (Oryzasativa L.) production as their efficiency remained untested. Alone as well as combined application of Se- and Si-NPs (5, 10 and 20 mg L) was achieved along with CK. All the treatments significantly reduced the Cd and Pb contents in brown rice, except CK, Se3, Si1 and Se1Si3. Combined application of Se and Si (Se3Si2) was more effective in reducing the Cd and Pb contents by 62 and 52%, respectively. In addition, foliar application of both NPs improved the rice growth and quality by increasing the grain yield, rice biomass, and Se contents in brown rice. Highest concentration of Se (1.35 mg kg) in brown rice was observed with combined application of Se- and Si-Nps (Se3Si2). Selenium speciation revealed the presence of organic species (74%) in brown rice. The combinations of different doses of Se- and Si-Nps are the main determining factor for total concentration of metals in grains. These results demonstrate that foliage supplementation of Se and Si-Nps alleviate the Cd and Pb toxicity by reducing the metals' concentration in brown rice. Additionally foliage supplementation improved the nutritional quality by reducing the phytic acid contents in rice grains.