<p>The effect of endophytic fungal biotransformation on the formation of metabolic substances has become a non-negligible factor in assessing the quality of medicinal plants. However, the relevant evidences are still particularly lacking. In this study, an endophytic fungus CA3-A with biotransformation activity was screened and identified as <i>Talaromyces coprophilus</i> from root of <i>Astragalus mongholicus</i>. Its biotransformation effect on host metabolism was studied by co-culture with fungus and host root. The results showed that in addition to the significant changes in primary metabolites, secondary metabolite conversions are mainly focused on compounds such as terpenoids, phenols and flavonoids. The transformed metabolic pathways are mainly enriched in glycerophospholipid metabolism, ubiquinone and terpenoid quinones biosynthesis, and tyrosine metabolism. A total of <b>38</b> signature differential metabolites are found through multivariate statistical analysis. In addition to eleven primary metabolites including glycerides and glycerophospholipids, twenty-eight secondary metabolites distribute in terpenes, sterols, phenols, flavonoids, benzene, lipids and other classes of compounds, respectively. In conclusion, this study aims to quickly focus on the signature differentially metabolites from a large amount of information, narrow the possible range of potential transformation products, and provide help for understanding of influence of endophytes on host metabolism and the search for new natural products.</p>