This paper reports a well-designed and in-depth comparative study on the polysaccharide yields, contents, and antioxidant activities of two Hippophae species of great research value, namely, Hippophae rhamnoides subsp. sinensis Rousi and Hippophae gyantsensis (Rousi) Y. S. Lian. The total polysaccharides of H.rhamnoides subsp. sinensis and H. gyantsensis were obtained through hot water extraction. Yields were compared, and polysaccharide contents were accurately determined through phenol-sulfuric acid colorimetry and compared. Meanwhile, the antioxidant activity of the polysaccharides was evaluated through 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging. Results showed that the polysaccharide yield (percentage of crude extract relative to the raw material) of H.rhamnoides subsp. sinensis (1.18% ± 0.02%) was significantly lower than that of H. gyantsensis (3.12% ± 0.06%) (P 0.05). This experiment clarified the differences in polysaccharide yield, content, and antioxidant activity between H.rhamnoides subsp. sinensis and H. gyantsensis. This work can provide a scientific basis for the quality evaluation of sea buckthorn and the further development of polysaccharide active components.