The purpose of this paper was to investigate the effects of Cyclocarya paliurus polysaccharide (CP) on gut microbiota composition and predict metabolic function in healthy mice. Healthy Kunming mice were continuously gavaged with CP for 20 days, and mouse feces were collected for analysis. The results showed that CP could remarkably increase the short-chain fatty acids (SCFAs; acetic acid, propionic acid, butyric acid, and valeric acid) in the feces of healthy mice in a dose-dependent matter. 16S rRNA showed that 200 mg/kg body weight CP was effective in increasing diversity of the gut microbiota in healthy mice and affected the relative abundance of specific bacteria. Lachnospiraceae, Clostridiales, and Clostridia were identified as the phenotypic biomarkers of the CP-H group compared with the normal control group. In addition, PICRUSt2 showed that starch and sucrose metabolism, amino acid metabolism, glycerolipid metabolism, pantothenate and CoA biosynthesis, biosynthesis of unsaturated fatty acids, and C5-branched dibasic acid metabolism are the primary enriched phenotypic KEGG pathways in the CP-H group. These findings suggested that early CP intervention could enhance the metabolic function of gut microbiota by increasing the release of SCFAs and altering the composition of gut microbiota.