Objective: To compare the clinical efficacies between endoscopic minimally invasive polypectomy with gallbladder preservation and laparoscopic cholecystectomy in treatment of gallbladder polyps. Methods: One hundred and ninety-six patients with gallbladder polyps who met our criteria were designated to undergo either endoscopic minimally invasive gallbladder preserving polypectomy (gallbladder preservation group, 103 cases) or laparoscopic cholecystectomy (cholecystectomy group, 93 cases) depending on the their own willingness. The intra- and postoperative conditions of the patients between the two groups were compared. Results: There were no significant differences between the two groups with regard to age, sex and comorbidities (all P>0.05), so they were comparable. Two patients in gallbladder preservation group were converted to perform cholecystectomy due to gallbladder wall hemorrhage after polypectomy. Compared with cholecystectomy group, in gallbladder preservation group, the average operative time and intraoperative blood loss were reduced [(50.3±12.9) min vs. (61.2±16.7) min; (10.2±2.7) mL vs. (15.1±3.9) mL]; the incidences of postoperative pain and gastrointestinal adverse reactions were decreased, and time to the first intestinal gas passage was shortened [16.83% vs. 32.26%; 18.81% vs. 3.33%; (18.5±4.1) h vs. (26.2±5.3) h]; the incidence of long-term complications were also decreased (10.89% vs. 22.58%) (all P<0.05). Conclusion: The minimally invasive endoscopic gallbladder preserving polypectomy has the advantages of less pain, fast recovery and fewer complications compared with laparoscopic cholecystectomy, and so it is a safe and effective treatment method for patients with suitable indications.