Abstract:using the goal programming model, using the 2008-2017 provincial panel data in China, the analysis of the transformation and upgrading of industrial structure, financial innovation of science and technology and the comprehensive effect of regional economic development, and to the transformation and upgrading of industrial structure and the financial innovation of science and technology to test the regional difference of economic development.The analysis results show that the transformation and upgrading of industrial structure on regional economic development, national, central and western provinces the comprehensive effect of transformation and upgrading of industrial structure;Financial technology innovation driving effect on transformation and upgrading of industrial structure, the financial innovation of science and technology to promote transformation and upgrading of industrial structure, the transformation and upgrading of industrial structure, in turn, promote regional financial technology innovation and regional financial innovation of science and technology, in turn, promote the development of regional economy, regional economic development and further promote transformation and upgrading of industrial structure, the three blend mutually promote each other, promote the development of national scientific and technological innovation, promote economic and social quality, and the efficiency.