Objective: To observe the effect of Yiqi Tongfu Decoction combined with etimicin Injection in the treatment of gastrointestinal dysfunction caused by sepsis. Method: 66 patients with gastrointestinal dysfunction due to sepsis admitted to our hospital from December 2022 to April 2025 were selected as the research subjects. The patients were divided into the control group and the observation group by random number table method, with 33 cases in each group. The control group was treated with etimicin injection. The observation group was treated with Yiqi Tongfu Decoction on the basis of the control group. The therapeutic effects, severity of the disease (APACHE-II score), degree of gastric function impairment (AGI score), and infection-related indicators [Procalcitonin (PCT), total White Blood Cell count], inflammatory markers [Tumor Necrosis Factor-alpha (TNF-α), serum C-Reactive Protein (CRP), Interleukin-6 (IL-6)] and the occurrence of adverse reactions of the two groups were analyzed and compared. Result: The total effective rate of treatment in the observation group was significantly higher than that in the control group (P < 0.05). After 7 days of treatment, the APACHE-II scores of both groups were significantly lower than those before treatment, and the APACHE-II score of the observation group after treatment was significantly lower than that of the control group (P < 0.05). After 7 days of treatment, the AGI grades were significantly improved compared with those before treatment, and the AGI grade of the observation group after treatment was significantly better than that of the control group (P < 0.05). After 7 days of treatment, the PCT and WBC of both groups were significantly lower than those before treatment, and the PCT and WBC of the observation group after treatment were significantly lower than those of the control group (P < 0.05). After 7 days of treatment, the levels of TNF-α, CRP and IL-6 in both groups were significantly lower than those before treatment, and the levels of TNF-α, CRP and IL-6 in the observation group after treatment were significantly lower than those in the control group (P < 0.05). There was no significant difference in adverse reactions between the two groups during the treatment period (P > 0.05). Conclusion: The combination of Yiqi Tongfu Decoction and etimicin Injection in the treatment of gastrointestinal dysfunction caused by sepsis can improve the therapeutic effect, alleviate the symptoms of patients, reduce infection and inflammation, and has good safety.