The current study aimed to synthesize nitrogen-doped quantum dots (NQDs) and to study their effect on germination and drought tolerance of two rice cultivars (Sakha Super 300 and Sakha 108) at seedling stage. Microwave-assisted carbonization of glucose in presence of ammonia was followed to obtain NQDs that were characterized by spectral analysis, FTIR, electron microscopy, zetametry, elemental analysis and cytotocicty assessment. Grains of the two rice cultivars were primed in NQDs then germination rate and seedling growth parameters were determined under control and polyethylene glycol-induced drought. Also, the effect of grain priming on membrane features, activity of antioxidant enzymes, H2O2 content and the amount of some drought responsive metabolites was evaluated. The formed NQDs possessed blue luminescence under UV radiation with absorption peak at 275 nm. These NQDs had plenty of hydrophilic oxygen-containing groups with various C–N bonds. NQDs had an average size of 9.4 nm, zeta potential of -16.8 mV, O/C atomic ratio of 52%, and N/C ratio of 40%. NQDs proved to be non-toxic on four human cell lines. Grain priming of the two rice cultivars in NQDs enhanced their germination and ameliorated the ill impact of drought on germination rate as well as seedling length, biomass, and water content. Also, NQDs reduced injury to cellular membranes, reduced H2O2 content, and activated catalase, peroxidase, and superoxide dismutase. Moreover, NQDs increased seedlings content of trehalose, proline, phenols, and ascorbic acid. The easily prepared, highly stable, and safe-by-design NQDs can be applied to boost germination and drought tolerance of rice seedlings.