Objective To investigate the effects of Fuzheng Jiedu Prescription combined with enteral nutrition on TCM syndrome scores and tongue coating microbiota in gastric cancer patients with malnutrition. Methods A total of 86 gastric cancer patients with malnutrition were selected from Zhengzhou Hospital of Traditional Chinese Medicine from January 2022 to December 2023. According to the computer grouping method, they were divided into control group (43 cases, these patients were given enteral nutrition support treatment) and observation group (43 cases, these patients were treated with the addition of Fuzheng Jiedu Prescription treatment based on the control group). TCM syndrome scores, nutritional status, tongue coating microbiota and safety of the two groups were observed. Results Before treatment, there was no significant difference between the two groups in body emaciation, pale complexion, fatigue, epigastric pain and pale tongue coating (P>0.05). After treatment, the scores of body emaciation, pale complexion, fatigue, epigastric pain and pale tongue coating in the observation group were significantly lower than those in the control group (P<0.05). Before treatment, there was no significant difference in HGB, TRF, PAB and ALB levels between the two groups (P>0.05). After treatment, the levels of HGB, TRF, PAB and ALB in observation group were significantly higher than those in the control group (P<0.05). Before treatment, there was no significant difference in the relative abundance of Firmicutes, Bacteroidetes, Fusobacteria and Proteobacteria between the two groups (P>0.05). After treatment, the relative abundance of Bacteroidetes, Fusobacteria and Proteobacteria in the observation group was significantly higher than that in the control group, while the relative abundance of Firmicutes was lower (P<0.05). During treatment, there was no difference in the incidence of toxic and side effects between the two groups (P>0.05). Conclusion Fuzheng Jiedu Prescription combined with enteral nutrition can alleviate symptoms, improve nutritional status and tongue coating microbiota in gastric cancer patients with malnutrition with good safety.