To compare the efficacy of endoscopic mucosal dissection(ESD) and endoscopic mucosal resection(EMR) in the treatment of early type Ⅱ esophagogastric junction neoplasm. Methods A retrospective analysis of 120 patients who underwent endoscopic surgery for early type Ⅱ esophagogastric junction tumors in our hospital from April 2017 to August 2019 were divided into ESD group(n=64) and EMR group(n=56). Regular follow-up after operation was performed to compare the operation time, hospital stay, tumor resection rate, postoperative complication rate, tumor recurrence rate and survival rate of the two groups. Results The operation time and hospitalization time of the EMR group were significantly lower than that of the ESD group, and the difference was statistically significant(P＜0.05). The postoperative complication rate in the EMR group was 5.36%, which was significantly lower than the 18.75% in the ESD group, and the difference was statistically significant(P＜0.05). The R0 resection rate and enbloc resection rate in the ESD group were 92.19% and 95.31%, respectively, which were significantly higher than the 76.29% and 80.36% in the EMR group. The differences were statistically significant(P＜0.05). The local recurrence rate and the remote recurrence rate of the EMR group were higher than the ESD group, and the difference was statistically significant(P＜0.05). Conclusion ESD treatment of early type Ⅱesophagogastric junction neoplasm takes longer time than EMR surgery, and has a higher incidence of postoperative complications, but the surgical effect is better.