Aim This study investigated the cost-effectiveness of a community-based colorectal cancer-screening program (C-CRCSP) in Shanghai, China, with a comparison of urban, suburban, and rural areas. Methods A Markov model was constructed to evaluate the cost-effectiveness of a 25-year-long annual C-CRCSP with 100,000 samples. Cost-effectiveness was determined by the incremental cost-effectiveness ratio (ICER) referring to either life-years gained, or quality-adjusted life-years (QALYs) gained. The threshold was gross domestic product per capita. Univariate and multivariate sensitivity analyses were performed to investigate the influence of compliance, prevalence, technological performance, price, and an annual cost discount rate (3.5%) on ICERs. A probabilistic sensitivity analysis evaluated the probability of cost-effectiveness of C-CRCSP at different maximum acceptable ceiling ratios. Results Compared with no screening, the C-CRCSP could result in total gains of 7840 QALYs and 2210 life-years, at a total cost of CNY 58.54 million; that is, the ICERs were CNY 7460/QALY and CNY 26,650/life-year. Stratifying by residency, the highest cumulative gains in QALYs and life-years were estimated for the rural population, followed by the suburban and urban. The cost for the urban population was 3- and 6-fold that of the suburban and rural populations. The ICERS for QALYs ranged from 2180 (rural) to 16,840 (urban). Conclusion The cost-effectiveness of a C-CRCSP in Shanghai was most favorable for the rural population, while the urban population would realize lesser benefit in terms of QALYs. ICERs could be enhanced by measures that increase compliance. This article is protected by copyright. All rights reserved.