To investigate the effects of different doses of elemene emulsion injection on virus in the feces of rats.Methods:Eighteen specific pathogen-free healthy male Sprague-Dawley(SD) rats were randomly divided into three groups：low-dose elemene emulsion injection group [L-EEI，20 mg/(kg·d)]，high-dose elemene emulsion injection group [H-EEI，40 mg/(kg·d)] and Control group(equal volume of normal saline)，with six rats in each group.After 14 days of continuous administration，fresh feces were collected for metagenomic sequencing，followed by bioinformatic analysis of the detected viruses.Results:Venn diagram analysis showed that the number of unique viruses in control，L-EEI and H-EEI groups were 6，6 and 10，respectively，with 77 common viruses identified at the species level across the three groups.PCA analysis showed that the data of the L-EEI group were significantly different from those of the other groups(P=0.036 at the genus level，P=0.012 at the species level).NMDS analysis showed that the degree of data aggregation in L-EEI and H-EEI groups was higher(genus level：Stress=0.093，species level：Stress=0.129).A total of 10 viruses showed significant differences among the three groups(P<0.01).The effects of different doses of EEI on viral abundance could be divided into three categories：1) viral abundance was positively or negatively correlated with EEI dose; 2) Compared with the control group，L-EEI increased virus abundance，but H-EEI had no significant effect on virus abundance;3) Compared with the control group，L-EEI caused a decrease in virus abundance，but H-EEI had no significant effect on virus abundance.Conclusion:Different doses of EEI could induce changes in the composition and structure of the virus in the feces of rats，and different viruses show varying sensitivities to different doses of EEI.