Background Chronic obstructive pulmonary disease (COPD) represents a significant public health challenge. This study aimed to investigate the epidemiological characteristics of COPD across different altitudes and evaluate the potential influence of altitude on its prevalence of high-risk populations. Methods This cross-sectional study employed a multi-stage randomized cluster sampling method and enrolled 11,095 adult residents aged >= 20 years at different elevations in Yunnan Province, China. Screening questionnaires identified high-risk individuals among participants, who then underwent pulmonary function tests. COPD was diagnosed based on post-bronchodilator test results. We utilized multivariate logistic regression models to examine the association between altitudes and COPD prevalence while controlling for demographic variables, lifestyle factors, and disease characteristics. Results A total of 2,252 (20.3%) were in the high-risk group. The prevalence of COPD in high-risk populations increased with age across low, intermediate, and high altitude areas. COPD patients in high-risk populations at high-altitude areas had a higher prevalence of ethnic minorities and significant biomass fuel exposure. Conversely, the proportion of COPD patients in the severe stages (GOLD III-IV) was notably lower in high-altitude regions. Logistic regression models revealed COPD prevalence in high-risk populations at high altitudes to be significantly lower than at low altitudes, with odds ratios of 0.538(95% CI: 0.343-0.844), 0.470(95% CI: 0.289-0.766), and 0.518 (95% CI: 0.316-0.848) for Models 1, 2, and 3, respectively (all P < 0.05). Conclusion The prevalence of COPD in high-risk populations is the lowest in the high-altitude regions of Yunnan Province, and high altitude is an independent factor negatively associated with COPD.