Innovation is the first power that lead the development. However, due to the lack of industry data, there is little research on the scale of innovation economy. Based on the industry data of Fujian Province input-output table, the direct and indirect contribution of Fujian Innovation Industry to economy was studied. By classifying the degree of industry innovation, the input-output table 42 sectors are divided into category a completely high innovative industries, category B partially high innovative industries and other industries.The result shows that the direct contribution of innovation to the economy in 2017 is between 11.68% and 34.88% , and the indirect contribution is between 15.53% and 43.27% . The indirect contribution of innovation to economy is greater than the direct contribution, and there is a clear spillover effect in the development of innovation economy in Fujian Province. From 2002 to 2015, the overall innovation capacity of Fujian Province continued to decline slowly. After 2015, the decline trend was reversed, and at present the innovation situation of Fujian province is still very severe.