Natural polysaccharides have unsatisfactory properties in production and processing due to structural limitations. Recent studies have shown that chemical modifications can improve the physicochemical and functional properties of plant polysaccharides. Herein, the effect of selenylation on the structure, functional properties, and in vitro digestion characteristics of yam polysaccharide (YP) was investigated. Selenylated products with different selenium contents (YP-LSe and YP-HSe) were prepared by controlling the addition of sodium selenite, and all samples were identified as acidic polysaccharides. Selenylation induced alterations in the chemical composition of YP. FT-IR spectral analysis revealed that YP-LSe and YP-HSe exhibited characteristic vibrational absorption peaks associated with selenium-containing groups. Microstructure analysis showed that YP-LSe and YP-HSe presented stacked leaf-like structures with sphere attachments. Moreover, selenylation significantly enhanced the emulsion capacity, foaming capacity, and antioxidant capacity of YP. In the simulated digestion process, YP-LSe and YP-HSe exhibited greater resilience against the gastrointestinal environment than YP. This study provides a theoretical basis for the development and utilization of selenylation of YP in the field of functional foods.