Objective To investigate the factors influencing outcomes in patients with familial adenomatous polyposis (FAP) undergoing endoscopic polypectomy, so as to provide evidence for the endoscopic treatment of FAP-related colorectal polyps. Methods Clinical data of 35 FAP patients who underwent endoscopic polypectomy in The First Affiliated Hospital of Naval Medical University from Dec. 1998 to Jan. 2024 were retrospectively analyzed. Patients were categorized into attenuated FAP (AFAP, 20-99 polyps), sparse classic FAP (sCFAP, 100-999 polyps), and dense classic FAP (dCFAP, ≥1 000 polyps) based on the total number of polyps identified during the first complete colonoscopy. Treatment sessions, treatment duration, number of polyps removed, treatment costs, complications, compliance, and outcomes were compared among groups. Results The 35 FAP patients received a median of 5.0 (3.0, 6.0) endoscopic treatments over a period of 29.5 (20.0, 46.0) months. A total of 13 549 polyps were removed using various techniques: coagulation (3 148), biopsy forceps (957), snare (9 216), endoscopic mucosal resection (EMR) (206), endoscopic submucosal dissection (ESD) (2), and nylon ligation (20). Only 1 severe complication, colonic perforation, occurred, without massive hemorrhage. Sixteen patients discontinued endoscopic treatment at our hospital for various reasons. The 35 patients were classified into AFAP (7 cases), sCFAP (17 cases), or dCFAP (11 cases) groups. The AFAP group had the oldest age at initial diagnosis, lowest polyp burden, longest treatment intervals, but lowest costs; the sCFAP group had the highest proportion of females, most resected polyps, most treatment sessions, and highest costs; and the dCFAP group had the shortest treatment duration. During a median follow-up of 39 (23, 73) months, the risks of colorectal cancer (CRC), high-grade intraepithelial neoplasia (HGIN), and undergoing colectomy were the highest in dCFAP group and lowest in AFAP group. Conclusion Endoscopic treatment plays a crucial role in controlling polyp burden and preventing CRC in FAP patients, though its efficacy varies depending on initial polyp burden. AFAP patients benefit most from endoscopic therapy with relatively low costs and delayed surgical intervention. Some sCFAP patients have delayed surgery through more frequent and costly endoscopic treatments, although they carry a higher risk of polyp malignancy. dCFAP patients are less likely to undergo long-term endoscopic therapy and may require it as a temporary measure before surgery. Personalized monitoring and management strategies tailored to different types of FAP patients are essential.