Objective To analyze the prevalence of metabolic syndrome (MetS) and its risk factors between the elderly Yi and Han nationality population in Sichuan Province. Methods A cross-sectional survey was carried out in a representative sample of persons aged ≥20 years in Sichuan region from June 2007 to August 2007 with stratified cluster sampling method．The data of elderly Yi and Han nationality people aged ≥60 years were analysed. Results The prevalence of MetS in elderly Yi and Han nationality population was 23.6% and 29.0%, respectively, which were both higher in females than in males. The prevalence of MetS in male Yi people was higher than than that in male Han people. Yi people in rural area had significantly lower prevalence of MetS than those in urban area. In rural areas, the prevalence of MetS was strikingly lower in the elderly Yi people than in Han people. Female, age and urban residence were independent risk factors for MetS in the elderly Han people, while only female was independently correlated to MetS in the elderly Yi people. Conclusion Regardless of race, the prevalence of MetS was higher in female than in male. The urban residents of Yi people had higher prevalence of MetS than in rural counterparts, whereas the gap was not noted in Han people. The implementation of health strategies needs extensive development in elderly Yi and Han population.