To analyze the changes of the government financial input to Centers for Disease Prevention and Control (CDCs) at county level in China, 257 county-level CDCs were selected with systematic sampling. In 2002-2012, the annual growth rate of government financial input, personal expenditure and general operating expense was 19.5%, 15.4% and 18.2% respectively. And the growth rates of per capita of the above indicators were also high. The proportion of financial input in total spending of CDCs increased from 53.7% to 65.1% in 2002-2012, meanwhile, the proportion of income from paid service decreased relatively. And the proportion of institutions that government financial input could basically meet CDCs’ needs increased from 28.4% to 50%. As for the regional distribution, the east area growth rates in different indicators ranked first, and the middle area ranked last. In the future, Stable financial input mechanism of CDCs should be set up based on current total input and growth rate of financial resources. Additionally, we should pay more attention to the balance of different regions, especially in middle area. Last, it is suggested to ensure the input effect by consummating performance evaluation of CDCs at county level.