Natural polysaccharides are concerned for their high biological activity and low toxicity. Two kinds of polysaccharides were extracted from Hippophae rhamnoide L. by microwave-assisted aqueous two-phase system. Under the optimal conditions predicted by RSM model (K2HPO4/ethanol (18.93 %/28.29 %), liquid to material ratio 77 mL/g, power 625 W and temperature 61 degrees C), the yield of total polysaccharides reached 35.91 +/- 0.76 %. Moreover, the polysaccharides extraction was well fitted to the Weibull model. After purification by Sepharose6B, the polysaccharides from top phase (PHTP, purity of 81.44 +/- 1.25 %) and bottom phase (PHBP, purity of 88.85 +/- 1.40 %) were obtained. GC, FT-IR, methylation and NMR analyses confirmed the backbone of PHTP was composed of a repeated unit -> 4)-beta-D-Glcp-(1 -> 2)-alpha-L-Rhap-(1 -> 4)-beta-D-Galp-(1 -> 4)-alpha-D-GalAp-(1 -> 3)-alpha-LAraf-(1 -> 3)-alpha-D-Manp-(1 ->, while the repeated unit in PHBP was -> 3)-alpha-L-Araf-(1 -> 2)-alpha-L-Rhap-(1 -> 4)-beta-D-Glcp-(1 -> 3)-alpha-D-Manp-(1 -> 4)-beta-D-Galp-(1 -> 4)-alpha-D-GalAp-(1 ->. Compared with PHTP (6.46 x 106 g/mol), PHBP with relatively low molecular weight (8.2 x 105 g/mol) exhibited the smaller particle size, better water solubility, thermal and rheological property, stronger anti-glycosylation and alpha-amylase inhibitory effects. Moreover, PHTP and PHBP displayed a reversible inhibition on alpha-amylase in a competitive manner. This study provides a high-efficient and eco-friendly method for polysaccharides extraction, and lays a foundation for sea buckthorn polysaccharides as potential therapeutic agents in preventing and ameliorating diabetes.