Abstract: The paper selects 13 specific indicators to construct the evaluation index, which includes three hard elements, three levels of factor input, innovation support and innovation space, and two soft elements, which has two levels of market degree and innovation environment. In this study factor analysis was used to analyze the data of 31 regions, in order to achieve the goal of measuring and evaluating the government's governance ability of scientific and technological innovation. The result shows that the comprehensive scores of some southeast regions, such as Guangdong, Jiangsu, Beijing, Shandong, Shanghai and Zhejiang, are high. The governance ability of the central and western regions is generally weak. And the ability, which promotes the independent innovation of regional enterprises, needs to be improved.