Abstract: Vaccine is the most effective method to prevent the spread of communicable diseases, but the immune response it induces varies significantly among individuals and populations in different regions. Recent studies have shown that the composition and function of the gut microbiota play a key role in the immune response following vaccination. This article aims to explain the differences in gut microbiota among different vaccinated populations and animals, discuss how the gut microbiota affects the immune efficacy of the vaccine, and summarize strategies for targeting the gut microbiota to improve vaccine efficacy.