Objective To evaluate the efficiency and safety of modified endoscopic anti-reflux mucosectomy (ARMS) for refractory gastroesophageal reflux disease (rGERD) with moderate hiatus hernia. Methods A total of 30 patients with rGERD with moderate hiatus hernia (3-5 cm) diagnosed at the Department of Gastroenterology of Northern Jiangsu People''s Hospital from June 2017 to June 2020 were randomly divided into 2/3 circumferential mucosal resection group (n=15) and 3/4 circumferential mucosal resection group (n=15) using random number table method, and received modified ARMS of the corresponding mucosal resection range. The GERD symptoms, esophagitis under endoscopy, 24 h pH results, and lower esophageal sphincter (LES) resting pressure were compared before and after the procedure. The therapeutic effect and complications of the two groups were analyzed. Results In 2/3 resection group, the GERD questionnaire scores (9.53±0.36 VS 11.93±0.57, t=6.874, P<0.001), acid exposure time (19.81%±1.72% VS 31.45%±2.78%, t=8.020, P<0.001) and the DeMeester score based on 24 h esophageal pH monitoring (40.98±4.55 VS 55.33±5.65, t=6.408, P<0.001) at 6 months after the treatment showed a significant reduction compared with those before. In 3/4 resection group, the GERD questionnaire scores (9.0±0.57 VS 12.47±0.68, t=8.650, P<0.001), acid exposure time (20.07%±2.19% VS 29.96%±3.00%, t=7.444, P<0.001) and the DeMeester score (33.67±3.47 VS 51.17±6.03, t=4.973, P<0.001) at 6 months after the treatment were lower than those before. There was no significant difference in the GERD questionnaire scores (t=0.790, P=0.436), acid exposure time (t=0.093, P=0.926) or the DeMeester score (t=1.278, P=0.212) between the two groups at 6 months after treatment. In the two groups, there was no significant difference in the ratio of esophagitis grade C and D (10/15 VS 5/15, χ2=3.894, P=0.063; 8/15 VS 4/15, χ2=2.778, P=0.125) or LES resting pressure [3.29 (2.66,8.29) mmHg VS 3.98 (3.67,9.43) mmHg, P=0.334;5.78 (1.9,8.46) mmHg VS 5.88 (3.28,8.99) mmHg, P=0.125] before and after the treatment. No postoperative delayed bleeding or perforation was observed. The incidence of postoperative esophageal stenosis of 2/3 resection group was lower than that of the other group (1/15 VS 6/15, χ2=4.658, P=0.021). Conclusion Modified ARMS is effective for controlling reflux symptoms and esophageal acid exposure in rGRED patients with moderate hiatus hernia (3-5 cm), but cannot significantly increase the postoperative resting pressure of LES. Compared with 3/4 circumferential mucosal resection, 2/3 circumferential mucosal resection can reduce the incidence of postoperative esophageal stenosis.