Aim: This study used a secondary database to analyze the changes in the prevalence and incidence of diabetes in Taiwan and the trend in the prevalence and incidence of diabetes in counties and cities. Method: Subjects with diabetes diagnosis and the use of blood glucose control agents were defined as diabetes, and NHI database LHID-2000 was used as sample to analyze the trend of the prevalence and incidence of diabetes from 2000 to 2012. Result: The annual prevalence of diabetes increased from 3.96% to 8.63% over the 13-year period of the study. The incidence rate increased from 0.95% in 2001 to 1.21% in 2012. The prevalence and incidence of male are higher than female. The prevalence and incidence of diabetes in counties and cities have negative correlation with the annual income and education level of residents in counties and cities. Conclusion: Each local government should promote diabetes prevention and control programs for different ethnic groups in accordance with the demographic characteristics of the county and city.