Scutellaria barbata D. Don has been used in traditional Chinese medicine for its heat-clearing and detoxifying effects to treat colitis. Polysaccharides are key bioactive constituents of S. barbata. In this study, a heteropolysaccharide (SBP80) was extracted from S. barbata using water extraction methods. In vivo mouse studies demonstrated that SBP80 exhibited significant therapeutic effects on ulcerative colitis (UC). Specifically, SBP80 improved body weight and disease activity index (DAI) scores in mice with UC, restored colon length, alleviated inflammatory cell infiltration in colonic tissues, and suppressed the levels of inflammatory cytokines and oxidative stress factors. Following purification, SBP80 yielded two polysaccharides, SBP80-1 (7.2 kDa) and SBP80-2 (292.3 kDa). Structural analysis revealed that both SBP80-1 and SBP80-2 were primarily composed of mannose, rhamnose, glucuronic acid, glucose, and galactose, with minor amounts of xylose, arabinose, and fucose. In addition, SBP80-2 contained higher amounts of glucuronic acid and xylose compared to SBP80-1. Methylation analysis further showed that the proportion of terminal sugar residues and 1,6-linked residues in SBP80-2 was higher, while SBP80-1 exhibited more 1,4-linked residues. In vivo zebrafish experiments demonstrated that both SBP80-1 and SBP80-2 inhibited intestinal length reduction and neutrophil infiltration in zebrafish with UC. They also reduced nitric oxide (NO) and reactive oxygen species (ROS) levels. Moreover, SBP80-2 exhibited superior anti-UC activity, which may be attributed to its structural characteristics. In conclusion, our findings indicate that S. barbata polysaccharides (SBP80-1 and SBP80-2) may be promising natural agents for the treatment of UC.