The work aims to introduce the main active ingredients of Hippophae rhamnoides Linn. and the research progress of their effects on gastrointestinal microbes. The main active ingredients in Hippophae rhamnoides Linn. and the gastrointestinal micro-ecological system were expounded. The research on the relationship between Hippophae rhamnoides Linn. and human gastrointestinal microorganisms was analyzed, and the future development prospects were prospected. Hippophae rhamnoides Linn. was rich in active ingredients such as polyphenols, vitamins, lipids, terpenoids, steroids, polysaccharides, proteins, peptides, and amino acids, which had a good effect on the inhibition of a variety of pathogenic microorganisms and the potential to improve the potential of the intestinal micro-ecological system. From the perspective of the future development trend, Hippophae rhamnoides Linn. has far-reaching research value in improving the gastrointestinal micro-ecological system disorder and food storage, and will have a broader development prospect.