To investigate the effects of Rhizoma Coptidis(RC) on the intestinal microbiota of female rats for reference in the rational clinical use of RC.Methods:Eight-week-old female rats were administered with different doses of RC decoction by gavage.The specimens of duodenum，jejunum，ileum，and colon(including intestinal content) were collected at 1，2，and 3 weeks.The changes in the structure and quantity of five dominant intestinal microbiota，including Enterococcus，Escherichia coli，Bacteroides，Lactobacilli，and Clostridium，were observed by qRT-PCR technology.Results:In the duodenum，RC significantly promoted the growth of Enterococcus(P<0.05) while exhibiting a biphasic effect on Escherichia coli，Bacteroides，Lactobacilli，and Clostridium，initially promoting their growth，followed by inhibition(P<0.05).In the jejunum，RC demonstrated inhibitory effects on Enterococcus，Escherichia coli，Bacteroides，Lactobacilli，and Clostridium(P<0.05).In the ileum，RC promoted the growth of Enterococcus and showed a biphasic effect on Escherichia coli and Lactobacilli(P<0.05)，while inhibiting the growth of Bacteroides and Clostridium(P<0.05).In the colon，RC inhibited the growth of Enterococcus，Escherichia coli，Bacteroides，Lactobacilli，and Clostridium(P<0.05).In the duodenum，RC promoted the growth of Escherichia coli(P<0.05)，inhibited the growth of Enterococcus and Lactobacilli(P<0.05)，and exhibited a biphasic effect on Bacteroides and Clostridium(P<0.05).Notably，these promoting or inhibitory effects varied significantly depending on different administration doses，continuous administration durations，and intestinal segments.Conclusion:RC has a significant regulatory effect on the intestinal microbiota of female rats，and the degree of its effect varies significantly among different intestinal segments.This study offers new ideas and methods to enhance the understanding of the pharmacological action and mechanism of RC