Objective To compare the safety and effectiveness of underwater endoscopic mucosal resection (UEMR) versus conventional endoscopic mucosal resection (CEMR) for treating 6-9 mm diameters sessile protruding colorectal polyps. Methods Clinical data of 341 patients with 6-9 mm diameters sessile protruding colorectal polyps who underwent endoscopic resection were retrospectively analyzed. According to the surgical methods, patients were divided into CEMR group (218 cases, treated with CEMR) or UEMR group (123 cases, treated with UEMR). Propensity score matching (PSM) was used to match confounders at a 1∶1 ratio, ultimately resulting in 98 successfully matched pairs. Post-matching comparisons were made between the two groups regarding R0 resection rate, complete resection rate, operation duration, intraoperative bleeding volume, complications (perforation, postoperative abdominal pain), and the recurrence rate. Results After PSM, the UEMR group exhibited higher R0 and complete resection rates, shorter operation duration, less intraoperative bleeding volume, and a lower recurrence rate compared to the CEMR group (P<0.05). No statistically significant difference in the incidence rates of perforation and postoperative abdominal pain was observed between the two groups (P>0.05). Conclusion For 6-9 mm diameters sessile protruding colorectal polyps, UEMR offers superior resection completeness, shorter operation duration, reduced intraoperative bleeding volume, and a lower recurrence rate compared to CEMR, while maintaining comparable safety.