BRAF V600E-mutated colorectal cancer (CRC) is very aggressive and responds poorly to standard treatment. In this study, BRAFV600E-mutant mice with CRC were treated with intragastric cyasterone, a compound commonly used in traditional Chinese herbal medicine, for 21 days. Microbial DNA was extracted from mouse intestinal contents for 16S ribosomal RNA gene amplicon sequencing and analyzed. Our results indicated that cyasterone enhanced the diversity of the gut microbiota. The abundance of beneficial bacteria, such as Prevotellaceae, Muribaculaceae, and Ruminococcaceae was significantly higher in cyasterone-treated mice than controls. The abundance of Erysipelotrichaceae, a family of bacteria that promotes inflammation in the gut, was significantly positively correlated with tumor weight. Cyasterone is a potential inhibitor of BRAFV600E-mutant CRC via its effects on intestinal flora.