Objective To evaluate the effectiveness and safety of indocyanine green fluorescence method versus modified inflation-deflation method for thoracoscopic anatomic segmentectomy. Methods CNKI, Wanfang Database, China Biomedical Literature Database, Web of Science, Cochrane Library, EMbase, PubMed, Clinicaltrials.gov, were searched from 1 January 2000 to 1 May 2023, and controlled studies between indocyanine green fluorescence and modified inflation deflation method in thoracoscopic segmentectomy were collected. Meta-analysis was performed using Stata14MP and RevMan5.4. Results A total of 10 articles, including 1 156 patients, were identified. In thoracoscopic anatomic segmentectomy, indocyanine green fluorescence method had an advantage over modified inflation deflation method. The total incidence of postoperative complications decreased (OR=0.51, 95%CI 0.36 to 0.71, P<0.0001). The incidence of air leaks decreased (OR=0.50, 95%CI 0.31 to 0.80, P=0.004), the operation time shortened (MD=−25.81, 95%CI −29.78 to −21.84, P<0.00001), the length of postoperative hospital stays shortened (MD=−0.98, 95%CI −1.57 to −0.39, P=0.001), the rate of clear displaying for intersegmental boundary line increased (OR=5.79, 95%CI 2.76 to 12.15, P<0.00001). The difference was statistically significant. Conclusion Compared with modified inflation deflation method, indocyanine green fluorescence method can quickly and clearly display the intersegmental boundary line, reduce the difficulty of surgery, shorten the operation time, reduce the length of postoperative hospital stay, and provide reliably technical support for thoracoscopic anatomic segmentectomy. It is an effective and safe method, which is worthy of extensive application.