Abstract： Objective： To observe the clinical effect of modified Chaihu Guizhi Ganjiang Decoction combined with western medicine for functional dyspepsia complicated with irritable bowel syndrome (IBS) and its effect on intestinal flora in patients. Methods： A total of 60 cases of patients with functional dyspepsia complicated with IBS were divided into the control group and the observation group according to the random number table method，with 30 cases in each group. The control group was treated with routine western medicine ， and the observation group was additionally treated with modified Chaihu Guizhi Ganjiang Decoction based on the treatment of the control group. The traditional Chinese medicine (TCM) syndrome scores，Generic Quality Of Life Inventory- 74 (GQOLI- 74) scores and levels of gastrointestinal hormones and intestinal flora in serum were compared between the two groups. The clinical effects and the incidence of adverse reactions were evaluated in the two groups. Results： After treatment， the total effective rate in the observation group was higher than that in the control group (P＜0.05). After treatment， TCM syndrome scores including discomfort due to postprandial fullness， early satiety， and pain and burning sensation in the upper abdomen in the two groups were decreased when compared with those before treatment (P＜0.05)， and GQOLI- 74 scores were increased (P＜0.05)； TCM syndrome scores in the observation group were lower than those in the control group (P＜0.05)， and GQOLI- 74 score was higher than that in the control group (P＜0.05). After treatment， the levels of motilin (MTL) and cholecystokinin (CCK) in serum in the two groups were decreased when compared with those before treatment (P＜0.05)， and calcitonin gene- related peptide (CGRP) levels were increased (P＜0.05)； the levels of MTL and CCK in the observation group were lower than those in the control group (P＜0.05)，and CGRP level was higher than that in the control group (P＜0.05). After treatment， the levels of bifidobacterium and lactobacillus in the two groups were increased when compared with those before treatment， and the levels of enteric bacillus and enterococcus were decreased (P＜0.05)； the levels of enteric bacillus and enterococcus in the observation group were lower than those in the control group (P＜ 0.05)， and bifidobacterium and lactobacillus levels were higher than those in the control group (P＜0.05). There was no significant difference being found in the comparison of the incidence of adverse reactions between the two groups (P＞0.05). Conclusion：Modified Chaihu Guizhi Ganjiang Decoction combined with western medicine has a definite effect on the treatment of functional dyspepsia complicated with IBS bowel syndrone， which can effectively improve the gastrointestinal function of patients， regulate the balance of intestinal flora，and enhance the quality of life of patients.