Objective: To study the effects of Cistanche deserticola and its active components Cistanche deserticola polysaccharide and Echinacoside on intestinal flora of antibiotic-associated diarrhea (AAD) mice. Methods: Forty-eight Balb/c mice were randomly divided into control (Con) group, AAD Group, inulin (Inu) group, Cistanche deserticola (RCR) group, Cistanche deserticola polysaccharide (RCRDT) group and Echinacoside (Ech) group with 8 mice in each group. The diarrhea model of mice was induced by intragastric administration of lincomycin hydrochloride(3 g/kg) for 7 days, and then treated by intragastric administration of INU(5 g/kg), RCR(5 g/kg), RCRDT(200 mg/kg) and ECH (60 mg/kg),0.2 ml once a day for 7 days, Con group and AAD group were given the same volume of normal saline. By observing general signs of mice, colon HE staining, 16S rDNA high-throughput sequencing analysis, the effects of Cistanche deserticola, Cistanche deserticola polysaccharide and Echinacea glycoside on the imbalance of intestinal flora induced by antibiotics in mice were evaluated. Results: Compared with Con group, AAD group mice lost weight, presented obvious diarrhea symptoms, inflammatory changes in colon tissue and decreased intestinal flora diversity (P＜0.05) indicating the success of the model. Compared with AAD group, the weight and diarrhea of INU, RCR, RCRDT and ECH groups were significantly improved, and the colon pathology of ECH group was restored to normal level. Compared with AAD group, RCR group, RCRDT group and ECH group had significantly decreased intestinal Firmicutes, increased Blautia and Lachnoclostridium, and decreased Clostridium_sensu_stricto_1 (P＜0.05) . In ECH group, the abundance and diversity of intestinal microflora were returned to normal level, and the structure of intestinal microflora was well adjusted, the contents of Bacteroides, Flavonifractor, Agathobacter, Lachnoclostridium and Prevotella-9 were increased (P＜0.01). Conclusion: Both Cistanche deserticola and its active components cistanche deserticola polysaccharide and echinacoside can regulate the intestinal flora imbalance caused by antibiotics and improve the symptoms of AAD, especially echinacoside.