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Abstract Although silicon-based nanomaterials (Si-based NMs) can promote crop yield and alleviate biotic and abiotic stress, the underlying performance mechanisms are unknown. In the present study, the effect of the root application of Si-based NMs on the physiological responses of cherry radish (Raphanus sativus L.) was evaluated in a life cycle experiment. Root exposure to 0.1% (w/w) Si-based NMs significantly increased total fresh weight, total chlorophyll and carotenoids by 36.0%, 14.2% and 18.7%, respectively, relative to untreated controls. The nutritional content of the edible tissue was significantly enhanced, with an increase of 23.7% in reducing sugar, 24.8% in total sugar, and 232.7% in proteins; in addition, a number of nutritional elements (Cu, Mn, Fe, Zn, K, Ca, and P) were increased. Si-based NMs exposure positively altered the phytohormone network and decreased abscisic acid content, both of which promoted radish fresh weight. LC-MS-based metabolomic analysis shows that Si-based NMs increased the contents of most carbohydrates (e.g., α-D-glucose, acetylgalactosamine, lactose, fructose, etc.) and amino acids (e.g., asparagine, glutamic acid, glutamine, valine, arginine, etc.), subsequently improving overall nutritional values. Overall, nanoscale Si-based agrochemicals have significant potential as a novel strategy for the biofortification of vegetable crops in sustainable nano-enabled agriculture.