Objective To investigate the value of ultrasound, MRI and CT in the diagnosis of gastrointestinal lymphoma. Methods A total of 21 patients with gastrointestinal lymphoma who were admitted to the hospital from January 2011 to May 2016 were selected as the subjects. All patients were examined by ultrasonography, MRI and CT. Imaging findings of gastrointestinal lymphoma were observed. The diagnostic value of ultrasound, MRI and CT for gastrointestinal lymphoma was evaluated with the pathological findings of tissue biopsy as the golden standard. Results The accuracy rate of MRI in the diagnosis of gastrointestinal lymphoma (95.24%) was higher than that of ultrasound (80.95%) or CT (90.48%). Imaging findings of gastrointestinal lymphoma diagnosed by ultrasound, MRI and CT were characteristic. MRI plain scan only can visually display the gastric mucosal integrity, with certain reference value for the qualitative diagnosis of lesions. Compared with CT and ultrasound, it has more obvious advantages. In addition, T1WI and T2WI of MRI scancan clearly show the situation of gastric serosa, which was conductive to determining the depth of tumor invasion. Conclusion In the classification diagnosis of gastrointestinal lymphoma, the accuracy of MRI is higher than that of CT or ultrasound. It is suitable for clinical application.