The organic selenium (Se), particularly in the form of selenoamino acids, in non-edible sections or by-products of Se-enriched plants, has the potential to generate Maillard reaction products (MRPs) during thermal treatment or fermentation. To elucidate the recycling process of organic selenium in foods and improve the utilization rate of Se, the biotransformation of organic selenium was studied by the cultivation of edible radish sprouts with Se-MPRs. Maillard reactions were simulated using selenoamino acids (SeAAs; selenomethionine and methylselenocysteine) and reducing sugars (glucose and fructose) for preparing Se-MRPs. The structures of the possible dehydrated Se-MRPs were analyzed using a HPLC-ESI-MS/MS system based on their fragmentation patterns and Se isotopic characteristics. Se absorption by the radish sprouts cultivated using Se-MRPs was estimated by the corresponding Se in the SeAAs and the total Se contents. The capabilities of SeAA transformation and total Se assimilation by the sprouts were related to the substrate composition during the Se-Maillard reaction. A particular Se-MRP (selenomethionine + fructose) increased SeAAs transformation by 33.8% compared to selenomethionine. However, glucose and fructose seemed to inhibit the transformation of the Se-MRPs to SeAAs by 10.0 to 59.1% compared to purified Se-MRPs. These results provide key references for the efficient utilization of organic Se in the cultivation of Se-enriched sprouts.