Selenium (Se) is an essential trace element for the human body, and its dietary deficiency has been a widespread issue globally. Vegetables serve as a significant source of dietary Se intake, with organic Se derived from plants being safer than inorganic Se. In the present study, Taraxacum mongolicum plants were treated with various concentrations of Na₂SeO₃. The results showed that as the concentration of Na₂SeO₃ increased, the chlorophyll content of dandelion seedlings decreased at high concentrations, and the content of soluble sugars, soluble proteins, flavonoids, total phenols, and Vc all increased. The application of Na₂SeO₃ at concentrations ranging from 0 to 4 mg/L resulted in a reduction in plant malondialdehyde content and an enhancement in the activity of antioxidant enzymes. Following the Na₂SeO₃ treatment, five Se species were identified in the seedlings, Se⁴⁺, Se⁶⁺, selenocysteine, selenomethionine, and methylselenocysteine. Notably, selenomethionine emerged as the primary organic Se species in the shoots of dandelion. Transcriptome analysis revealed that ABC11b, PTR4, MOCOS, BAK1, and CNGC1 were involved in the absorption, transport, and storage of Se in dandelion, and C7317 was involved in the scavenging of reactive oxygen species. This study complements the understanding of the possible molecular mechanisms involved in the absorption and transformation of organic Se by plants, thereby providing a theoretical foundation for the biofortification of dandelion with Se in crops.