Objective To prospectively determine the diagnostic performance of 3.0T magnetic resonance imaging (MRI) routine sequence combined with intravoxel incoherent motion (IVIM) models in diagnosis of preoperative T staging and differentiating the pathological differentiated grade of esophagogastric junction adenocarcinoma. Methods Prospective study of 47 cases of patients with newly diagnosed adenocarcinoma of esophagogastric junction confirmed by electronic digestive tract endoscopy and surgical pathology results. All patients received conventional MRI plain scan and IVIM examination one weeks before operation. The images of IVIM were imported into the GE AW 4.6 workstation. Freehand ROI was used to cover the whole tumor volume, ADC, D, D* and f was calculated. Kappa consistency test was used to assess the consistency of T staging between the two methods. Results The accuracy of 3.0T magnetic resonance imaging (MRI) routine sequence combined with IVIM-DWI MRI for T stages was 85.77%, 71.43% for T1, 75% for T2, 88.24% for T3 and 93.33% for T4 and respectively. The ADC and D values had significant difference among the different histologic grade of AEGs (P<0.05), while the D* and f values had no difference(P>0.05). Conclusion 3.0T magnetic resonance imaging (MRI) routine sequence combined with intravoxel incoherent motion (IVIM) models has great significance for preoperative assessment of T staging and differentiating the pathological of esophagogastric junction adenocarcinoma.