Objective To explore the influencing factors of lymph node metastasis of Siewert Ⅱ/Ⅲ gastroesophageal junction adenocarcinoma (AEG) and its influence on prognosis of this kind of patients. Methods The clinical and pathological data of 49 patients with Siewert Ⅱ/Ⅲ AEG who admitted to Shiyan Hospital of Traditional Chinese from January 2010 to January 2013 were retrospectively analyzed. Univariate and multivariate analyses of factors affecting lymph node metastasis of AEG were performed by using a chi-square test and an unconditional logistic regression model; the effect of lymph node metastasis on the prognosis of patients with Siewert Ⅱ/Ⅲ AEG was performed by log-rank test. Results Multivariate unconditional logistic regression analysis showed that, tumor diameter (P=0.008), depth of invasion (P=0.019), vascular tumor thrombus (P=0.020), and degree of differentiation (P=0.017) were all influencing factors of lymph node metastasis. Patients with Siewert Ⅱ/Ⅲ AGE without lymph node metastasis had better survival than those with lymph node metastasis (P=0.005). Conclusion Tumor diameter, depth of invasion, degree of differentiation, and vascular tumor thrombus are independent risk factors for lymph node metastasis in patients with Siewert Ⅱ/Ⅲ AEG, and lymph node metastasis is associated with poor prognosis.