Selenium (Se) is a prerequisite metalloid for humans and animals. But, its essentialness or phytotoxicity is still obscure. Here, we investigated the dual effects of sodium selenite (0, 25, 50 or 100 μM) on the physio-biochemical, anatomical and molecular alterations in different Brassicca napus L. cultivars (viz. Zheda 619, Zheda 622, ZY 50, and ZS 758). Findings revealed that Se-supplementation markedly boosted the plant growth and biomasses by improving mineral uptake, water-soluble protein, sugar, photosynthetic efficiency regarding the pigments and gas exchange parameters. Higher Se-levels impaired the photosynthetic efficiency, deplete nutrients-uptake, osmotic stress by proline accumulation and higher Se-accumulation in roots led to growth and biomass reduction. Se-supplementation minimized the accumulation of ROS (hydrogen peroxide, superoxide radical), malondialdehyde and methylglyoxal (MG) levels by activating the enzymes engaged in AsA-GSH cycle and ROS-MG detoxification. But, elevated-Se impaired the oxidative metabolism by desynchronizing the antioxidants as revealed by decreasing levels of ascorbic acid, activities and expression levels of catalase, glutathione reductase, and dehydro-ascorbate reductase. Up-regulation of secondary metabolites genes (PAL, PPO) revealed the role of Se in regulating transcriptional networks involved in oxidative stress. The damages in leaf and root ultra-structures disclosed the Se-phytotoxicity. Together, outcomes uncovered the protective mechanism of Se (till 25 μM) by reinforcing the plant morphology, photosynthesis, osmo-protection, redox balance, enzyme activities for ROS-MG detoxification by reducing ROS and MG components. Excessive-Se prompt phytotoxicity by impairing above mentioned parameters, especially at 100 μM Se. Among all B. napus cultivars, Zheda 622 was discovered as highly-susceptible and ZS 758 showed greatest-tolerance against Se stress.