Objective: To explore the effect of the nursing intervention in patients with functional gastrointestinal diseases. Methods: 79functional gastrointestinal patients were selected from February 2015 to February 2016, and these patients were randomly divided into observation group and control group. 35 patients in each group. In the routine care of the medical department,the observation group has strengthened the comprehensive nursing care for the patient’s psychological, the living diet, the living environment, and the patient’s health education on the basis of the conventional nursing care. SCL-90 score was used to analyze the patient’s care and observe the health of the two groups after nursing care. Results: The scores of SAS and SDS were compared between the two groups after the intervention of the two groups. The scores of the two groups were decreased before the nursing intervention, the difference was statistically significant, but the trend of the observation group was more obvious. Compared with the control group, compared with before treatment there is a certain difference, the difference was statistically significant. Conclusion: In the comprehensive care of gastrointestinal patients, it can obviously improve the anxiety and depression of functional patients and improve the quality of life of patients.