Taking the national level innovative county-level city in Anhui Province as the research object, a coupling coordination model was used to analyze the relationship of coupling and coordination between regional innovation and high-quality development of county economy. It is found that between 2015 and 2020, the overall development level shows the fluctuation, and there are differences in regional innovation and high-quality economic changes.At the same time, the coupling coordination degree shows an upward trend, but the coordination level is low, indicating that regional innovation and high-quality economic development of county economy do not match, and regional innovation and high-quality economic development of county economy is in an unbalanced state.