Background Adenocarcinoma of esophagogastric junction (AEG) has a high incidence, while the extent of lymph node dissection (LND) and prognosis are still controversial. The present study aimed to explore the risk factors of lymph node metastasis (LNM) and prognosis in Siewert II/III AEG patients. Methods A total of 134 patients who underwent surgical operation between July 2013 and December 2019 at the Beijing Friendship Hospital were retrospectively reviewed. The patients were followed up until January 2020. The data were analyzed using logistic regression. Survival analyses were performed using Cox regression. Results Multivariate analysis revealed that the parameters infiltration depth (OR=4.341, 95%CI: 2.498-7.545, P=0.000), gross type (OR=3.626, 95% CI: 1.425-9.228, P=0.007) and intravascular cancer embolus (OR=2.888, 95%CI: 1.106-7.544, P=0.030) correlated with LNM. For all patients, the lymph nodes No. 1, 2, 3, 4, 7, 11 indicated higher lymph node metastatic rate in the abdominal cavity. However, No.5 and No. 6 indicated different tendency, which was higher in Siewert III AEG and lower in Siewert II AEG patients. Mediastinal LNM of Siewert II AEG mainly occurred in No. 110 and No. 111 cases corresponding to 7.1 and 3%, respectively, compared with those noted in Siewert III AEG patients. The 3-year overall survival analysis revealed that LNM ( P= 0.046) and chemotherapy ( P= 0.007) exhibited significant differences. Conclusion The infiltration depth, gross type and intravascular cancer embolus were independent risk factors of LNM. For Siewert II AEG patients, it is reasonable to remove both celiac and mediastinal lymph nodes. This was noted notably for No.1, 2, 3, 4, 7, 11, 110 and No.111. For No.5 and No.6 lymph nodes dissection was not required. For Siewert III AEG patients, mediastinal LND was not required. However, it was necessary to perform pyloric lymphadenectomy, which was performed for No.5 and No.6 lymph nodes. In addition, patients with LNM exhibited worse long-term prognosis. The data indicated that perioperative chemotherapy could improve the prognosis of AEG patients.