A field experiment was conducted to evaluate the efficiency of foliar application of different concentrations of Se fertilization (37.50, 56.25, 75.00, 93.75, and 112.50 g ha -1 of Se) at the early grain filling stage on nutritional quality of colored-grain wheat. The results showed that Se plays a role in influencing the nutrients concentration of colored-grain wheat. When it was more than 75.00 g ha -1 , the Se concentration in the common wheat was excessive. However, when it was more than 37.50 g ha -1 , the Se concentration in the colored-grain wheat was excessive, indicating that colored-grain wheat was likely to be more sensitive to Se accumulation. Se concentration of colored-grain wheat was significantly increased under the optimal foliar application of Se concentration at 37.5 g ha -1 , decreased starch concentration, without affecting the yield. Particularly, the concentrations of gliadin and glutenin were significantly increased while both albumin and globulin were reduced with the increased Se concentration. Additionally, our research showed that foliar application Se increased the concentration of iron (Fe), zinc (Zn), but decreased the concentration of copper (Cu) and manganese (Mn). More importantly, the intake of Se promoted the production of amino acids and anthocyanins. This indicates the potential roles Se plays on regulating nutrition value in colored-grain wheat.