Salvia yunnanensis is a traditional Chinese medicine for promoting blood circulation and eliminating blood stasis. Previous researches reported that Tanshinone IIA from Salvia yunnanensis had anti-angiogenic effect, however, whether its carbohydrates with similar effect is unknown. Here, we showed that a stachyose (Sta) from Salvia yunnanensis was purified by DEAE SepharoseTM Fast Flow anion-exchange chromatography and Bio-Gel P-2 gel permeation chromatography. Structure analyses suggested that Sta was tetrasaccharide as α-Gal-(1 → 6)-α-Gal-(1 → 6)-α-Glc-(1 → 2)-β-Fru. Further sulfated Sta was made and the degree of sulfate substitution was measured as 0.98. Bioactivity studies showed that Sta might block human microvascular endothelial cells tube formation in vitro and in vivo without significant cytotoxicity. Mechanism study suggested that Sta might bind to Galectin-3 (KD: 5.777E−6) and inhibit its expression to block angiogenesis linked to VEGFR/FAK and PDGFR/AKT/ERK signaling. Evidence also supported that Sta might be a potential compound for developing stachyose as an anti-angiogenesis functional food.