In our previous study, we found that Si Miao Formula (SMF) had the effect of improving the disorder of glucose metabolism caused by high fat and high sucrose diet, and significantly altered the composition of gut microbiota, especially increasing the level of Akkermansia muciniphila (A. muciniphila). However, it is unclear that the role of intestinal flora and A. muciniphila play in SMF improving blood glucose homeostasis, and the mechanism of how SMF increases the level of A. muciniphila. Therefore, this study will explore the correlation between SMF improving the insulin resistance and increasing the level of A. muciniphila, as well as the mechanism of SMF-induced growth of A. muciniphila using the in vitro and in vivo experiments. We explored the effect of intestinal flora and A. muciniphila on SMF-improved insulin resistance through fecal microbiota transplantation (FMT) and antibiotic intervention. In order to study the mechanisms underlying SMF on elevating A. muciniphila, we disassembled SMF to find the key component which can particularly elevate the number of A. muciniphila. Using the in vitro anaerobic culture system combined with cell and animal experiments, we explored the mechanism of the key component in elevating A. muciniphila. The research was approved by the Animal Ethical and Welfare Committee of Shanghai University of Traditional Chinese Medicine. Our results showed that the gut microbiota altered by SMF can improve high fat and sucrose diet induced insulin resistance in recipient mice, and the improvement was closely related to the abundance of A. muciniphila. Cortex Phellodendri played the most important role in regulating the composition of intestinal flora and increasing the number of A. muciniphila, of which, berberine was the key component of Cortex Phellodendri which up regulated A. muciniphila. We have found that berberine cannot directly promote the growth of A. muciniphila in vitro, but it can stimulate the expression of mucin, which, in turn, promote the growth of A. muciniphila. The above results show that the improved insulin sensitiviy by SMF depends on the increased level of A. muciniphila. The effect of SMF on elevating the amount of A. muciniphila might be correlated with the increased expression of mucin stimulated by berberine.