<p>Drought stress is a major constraint on the safe and stable production of rice, and the use of selenium (Se) to enhance crop stress resistance has emerged as a promising agronomic strategy. To examine the effects of different selenium forms and application methods on the drought tolerance of rice, this study applied selenite and nano selenium (Nano-Se) through seed coating and seed priming, respectively. Drought stress was simulated under hydroponic conditions using Polyethylene glycol-6000 (PEG-6000). The results showed that Nano-Se treatment was more effective in mitigating growth inhibition, optimizing root architecture, maintaining photosynthetic efficiency, and improving leaf water status. Among the treatments, seed priming with 5 mg L^− 1 Nano-Se produced the most pronounced benefits, performing significantly better than or comparable to the optimal selenite treatment. Notably, while enhancing selenium uptake, Nano-Se also reduced the accumulation of heavy metals (chromium, arsenic, cadmium, lead) in aboveground tissues under drought stress and helped maintain nutrient homeostasis. In contrast, high concentrations of selenite exhibited phytotoxic effects and potentially increased the risk of arsenic contamination. Overall, this study demonstrates that Nano-Se—characterized by low toxicity, slow-release behavior, and systemic regulatory functions—represents a highly promising novel formulation for improving drought resistance. These findings provide both theoretical insights and technical support for ensuring rice production safety and enhancing nutritional quality under complex environmental conditions.</p>