The potential of selenium-containing polysaccharides as organic selenium nutritional supplements has attracted considerable interest; however, they also encounter obstacles, including the presence of impurities and a low selenium binding efficiency. In this study, a novel method combining Q-Sepharose Fast-Flow (QFF) column chromatography with the HNO3–Na2SeO3 method was proposed. Through the application of this methodology, the selenium binding efficiency of polysaccharides was enhanced by a factor of 3.41. The selenium binding capacities of rhamnose and glucose were the highest among the monosaccharides, reaching 770.7 mg/L and 955.3 mg/L, respectively. Spirulina polysaccharide-3 (SPS-3) was selected for further investigation because of its elevated total rhamnose and glucose contents and optimal selenium binding efficiency. Employing common assays, a comparative analysis of selenium-containing Spirulina polysaccharide-3 (SeCSPS) and SPS-3 is presented. Upon selenium binding, the surface morphology of the monosaccharides changed, whereas the main chain structure remained unaltered. The antihyperglycemic activity of SeCSPS was enhanced by selenium binding. Furthermore, both SeCSPS and SPS-3 can be degraded by the simulated digestive system. In conclusion, SeCSPS can be employed as an organic selenium supplement in food or nutraceuticals while also resulting in a high selenium content. The findings of this study will provide a viable avenue for the high-value utilization of Spirulina, which will help resolve the selenium deficiency issue faced by populations with low selenium intake globally.