Se-enriched green tea has been widely used as a functional food and disease prevention. In this study, two kinds of homogeneous polysaccharides namely ASe-TPS2 and NSe-TPS2 were obtained from artificial and natural Se-enriched teas with the molecular weights of 6.73 × 103 Da and 2.44 × 105 Da. The structures of ASe-TPS2 and NSe-TPS2 were characterized by monosaccharide composition analysis, partial acid hydrolysis, methylation, FT-IR spectroscopy, NMR spectroscopy, SEM and TGA analysis. It showed that ASe-TPS2 and NSe-TPS2 were acidic polysaccharides containing high amount of uronic acid. The structure of the ASe-TPS2 was mainly composed of β‑D‑(1 → 3)‑Glcp, α‑D‑(1 → 4)‑GalpA, (1 → 4)‑Glcp, α‑L‑(1 → 2)‑Rhap and α‑D‑(1 → 4)‑GalpA, and the non-reducing ends were mainly composed of Araf and Xylp. However, the NSe-TPS2 was mainly composed of β‑D-(1 → 4)‑Glcp and α‑D‑(1 → 4)-GalpA, and the branches were mainly composed of β‑L‑(1 → 2)‑Araf, α‑D‑(1 → 3)‑Galp and β‑L‑(1 → 2)‑Rhap whereas the non-reducing ends were mainly composed of Glcp and Galp residues. These results suggested that the distinction of selenylation methods could present different polysaccharide chain structures.