At present, laparoscopic cholecystectomy (LC) is the main surgical treatment for gallstones. But, after gallbladder removal, there are many complications. Therefore, it is hoped to remove stones while preserving the function of the gallbladder, and with the development of endoscopic technology, natural orifice transluminal endoscopic surgery came into being. To compare the quality of life, perioperative indicators, adverse events after LC and transgastric natural orifice transluminal endoscopic gallbladder-preserving surgery (EGPS) in patients with gallstones. Patients who were admitted to The First Affiliated Hospital of Xinjiang Medical University from 2020 to 2022 were retrospectively collected. We adopted propensity score matching (1:1) to compare EGPS and LC patients. A total of 662 cases were collected, of which 589 cases underwent LC, and 73 cases underwent EGPS. Propensity score matching was performed, and 40 patients were included in each of the groups. In the EGPS group, except the gastrointestinal defecation (P = 0.603), the total score, physical well-being, mental well-being, and gastrointestinal digestion were statistically significant compared with the preoperative score after surgery (P < 0.05). In the LC group, except the mental well-being, the total score, physical well-being, gastrointestinal digestion, the gastrointestinal defecation was statistically significant compared with the preoperative score after surgery (P < 0.05). When comparing between groups, gastrointestinal defecation had significantly difference (P = 0.002) between the two groups, there was no statistically significant difference in the total postoperative score and the other three subscales. In the surgery duration, hospital stay and cost, LC group were lower than EGPS group. The recurrence factors of gallstones after EGPS were analyzed: and recurrence was not correlated with gender, age, body mass index, number of stones, and preoperative score. Whether EGPS or LC, it can improve the patient's symptoms, and the EGPS has less impact on the patient's defecation. It needed to, prospective, multicenter, long-term follow-up, large-sample related studies to prove.