This study systematically investigated the therapeutic effects of chemotherapy-induced mucositis (CIM) by cryptotanshinone (CTS) in mice. CIM mice were prepared by intraperitoneal injection of 5-fluorouracil (5-FU) and irinotecan for 4 days. A pseudo-sterile mouse model was established by intragastric administration of mixed antibiotics (metronidazole, vancomycin, and penicillin). The body weight, disease activity index (DAI), and defecation of mice were daily monitored. The animal welfare and experimental procedures followed the rules of the Animal Ethics Committee of the Institute of Materia Medica, Chinese Academy of Medical Sciences. We determined the contents of inflammatory factors, total cholesterol (TC), triglyceride (TG), and lipase activity in serum or colonic mucosa of CIM mice. We also studied the composition and relative abundance of fecal flora. The correlation of the relative abundance of fecal microbiota and environmental factors was further analyzed. CTS significantly decreased DAI and reduced the content of interleukin 6 (IL-6), interleukin 11 (IL-11), myeloperoxidase (MPO), and diamine oxidase (DAO) in the serum of CIM mice. CTS effectively increased the content of TG while reduced TC and lipase activity in serum. Results showed the incidence of CIM in pseudoaseptic model group was significantly reduced. Meanwhile, there was no significant difference in the contents of inflammatory factors and TG/TC ratio between pseudoaseptic model group and normal control group. There was a significant difference in the diversity and composition of fecal microbiota among groups. In addition, CTS restored the composition of fecal microbiota close to normal and significantly increased the abundance of g_norank_f_Muribaculaceae. Especially, g_Ruminiclostridium and g_norank_f_Muribaculaceae exhibited a significant positive correlation to TG but a negative correlation to DAO, MPO, IL-6, lipase, and TC. Cryptotanshinone significantly increased the abundance of g_norank_f_Muribaculaceae and g_ruminococcaceae_UCG-014 in fecal microbiota of CIM mice. In conclusion, we reported CTS effectively alleviated intestinal mucositis in mice induced by 5-fluorouracil and irinotecan by regulating fecal microbiota, inflammatory factors, and serum lipid.