An in-depth understanding of the Se uptake and metabolism in plants is necessary for developing Se biofortification strategies. Thus, hydroponic experiments were conducted to investigate the associated processes and mechanisms of organic Se [selenomethionine (SeMet) and selenomethionine-oxide (SeOMet)] uptake, translocation, transformation and their interaction in wheat, in comparison to inorganic Se. Results showed that Se uptake by roots and the root-to-shoot translocation factor under the SeMet treatment were higher than those under the selenite, selenate, and SeOMet treatments. The uptake and translocation of SeMet were higher than those of SeOMet within 72 h, although the differences gradually narrowed with time. The uptake of SeMet and SeOMet was also sensitive to the aquaporin inhibitor: AgNO3 addition resulted in 99.5% and 99.9% inhibition of Se in root in the SeMet and SeOMet treatments, respectively. Once absorbed by root, were rapidly assimilated to other Se forms, and SeMet and Se-methyl-selenocysteine (MeSeCys) were the dominant species in SeMet and SeOMet-treated plants, while notably, an unidentified Se form was also found in the root and xylem sap under the SeMet treatment. In addition, within 16 h, SeOMet inhibited the uptake and translocation of SeMet, while the interaction was weakened with longer treatment time. Taken together, the present study provides new insights for the uptake and transformation processes of organic Se within plants.