To study the effects of quinoa on intestinal microflora and short-chain fatty acid (SCFAs) metabolism in healthy mice. Select 40 SPF (Specific Pathogen Free) adult male mice were randomly divided into high， medium and low concentration gavage group and control group. The mice were administered intragastrically at 0.2 mL/2 d for 2 months. Collect the contents of the cecum of mice in the ninth week， extract the total DNA of the gut microbiota， amplify the V3-V4 region of the 16S rRNA gene through PCR， and analyze the sequencing data. SCFAs were extracted from the feces of mice at the ninth week by ethyl ether extraction method， and the changes of SCFAs in mouse feces were detected by high performance liquid chromatography. Quinoa has the effect of altering the overall structure of mice intestinal microbiota. The proportion of Firmicutes and Bacteroidetes in the intestinal microbiota of three test groups significantly increased at the phylum level compared to the control group after feeding with quinoa syrup. At the family level， quinoa significantly increased the relative abundances of Bacteroidetes S24-7_group， Lactobacillaceae， Prevotellaceae and Rikenellaceae， and decreased the relative abundances of Clostridiaceae 1， Clostridium vadinBB60 group and Lachnospiraceae. At the genus level， the dominant genera in the mouse gut were changed. The relative abundances of Prevotellaceae， Alloprevotella， Lactobacillus and Ruminococcus were significantly increased， while the relative abundance of Lachnospira was significantly decreased. The contents of acetic acid and propionic acid at the medium concentration were increased by 16.5% and 23.9% respectively compared with the control group. Quinoa can inhibit the growth of harmful bacteria in intestinal microbiota to a certain extent， and maintain the balance of intestinal microbiota by promoting the proliferation of probiotics and the production of SCFAs. The results lay a theoretical foundation for the development of quinoa functional foods， and provide scientific basis for future rational diet and personalized precise nutrition.