Abstract：Objective：To observe the clinical effect of modified Yinchen Wuling San on type 2 diabetes mellitus (T2DM) of spleen-deficiency and phlegm-damp type. Methods： A total of 27 cases of T2DM patients were randomly divided into the Metformin group (Group A)， the modified Yinchen Wuling San group (Group B) and the Metformin combined with modified Yinchen Wuling San group (Group C)，with nine cases in each group. After 28 days of treatment，fasting blood glucose (FBG) and scores of gastrointestinal adverse reactions in the three groups were compared before and after treatment； fecal samples were collected before and after treatment， respectively； high-throughput sequencing of fecal samples was performed by the PacBio sequencing platform； the abundance of microflora was compared among the three groups. Results：After treatment，FBG in the three groups was decreased (P＜0.05)，and there was no significant difference in the comparison of FBG among the three groups (P＞0.05). After treatment，the score of gastrointestinal adverse reactions in Group A was increased (P＜0.05)， and the scores of gastrointestinal adverse reactions in Group B and Group C were decreased (P＞0.05)； the score of gastrointestinal adverse reactions in Group A was higher than that in Group B and Group C (P＜0.05). After treatment，the abundances of ruminococcus (family level)，Clostridium (order level)，clostridia (class level) and Faecalibacterium prausnitzii (species level) in Group A were decreased (P＞0.05)， and the above abundances in Group B and Group C were increased (P＞0.05)， but there was no significant difference among the three groups (P＞0.05). Conclusion： Modified Yinchen Wuling San can reduce FBG， regulate intestinal flora disorder，increase the abundance of beneficial bacteria and protect gastrointestinal tract.