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ObjectiveTo analyze the cost-effectiveness of a colorectal cancer screening program using fecal DNA testing as initial screening in Wuhan, Hubei province, and to provide evidence for colorectal cancer screening decision making. MethodsWe collected detection results of 101 217 individuals who participated in a colorectal cancer screening program using stool DNA-based SDC2/AHDFE1/PPP2R5C methylation test as initial screening from October 20, 2021 to December 31, 2022 in Wuhan city. Patient costs associated with colorectal cancer screening and treatment were estimated through on-site surveys of 998 colorectal cancer patients at three tertiary hospitals in Wuhan city and a literature review of cost-effectiveness analyses of colorectal cancer screening. In addition, a sensitivity analysis was conducted to assess colonoscopy compliance among screened individuals. ResultsOf the 101 217 individuals who received the non-invasive colorectal cancer gene test, 4 483 (4.43%) were diagnosed with positive colorectal lesions and 3 200 underwent colonoscopy, of which 2 345 (71.38%) were found to have abnormalities. The total cost of the colorectal cancer screening program with fecal DNA testing was 34.8043 million Chinese yuan, the estimated total benefit was 297.5828 million yuan, and the estimated net benefit was 262.7785 million yuan, yielding a cost-benefit ratio of 1 : 8.55 for this screening program. Sensitivity analysis suggested that increasing colonoscopy compliance to 80%, 90%, and 100% could increase the cost-effectiveness ratio to 1 : 9.15, 1 : 9.78, and 1 : 10.36, respectively. ConclusionThe colorectal cancer screening program using fecal DNA testing for initial screening in Wuhan city has a high cost-benefit ratio, with increased colonoscopy compliance likely to result in even greater economic benefits.