Background: With the increasing prevalence of Siewert type Ⅱ adenocarcinoma of the esophagogastric junction (EGJ), the optimal surgical treatment is not universally agreed. This meta-analysis compares the safety and efficacy between the transhiahtal (TH) approach and the transthoracic (TT) approach. Methods: A systematic and electronic search of several databases was performed up to June 2020. The Newcastle-Ottawa scale was used to evaluate article quality and funnel plots were created to identify potential publication bias. The random-effects model was used when significant heterogeneity was identified. Results: In total, nine retrospective studies and two randomized controlled trials (RCTs) involving 2331 patients were included. Decreased intraoperative blood loss, shorter hospital stay, lower incidence of pulmonary complications, and longer 3-year overall survival were observed in the TH group. There were no significant differences concerning duration of surgery, R0 resection rate, number of dissected lymph nodes, perioperative mortality and morbidity rate, abdominal complication rate, or anastomotic leak rate. With regard to 5-year overall survival, a potential benefit may be achieved with the TH approach, which requires further confirmation. Conclusion: In terms of surgery-related and long-term outcomes, the TH approach may be more appropriate for Siewert type Ⅱ adenocarcinoma of EGJ, especially for esophagus invasion ≤4 cm.