Abstract:Systems and technology are two key to build long-term mechanism of clean government. Introducing innovative collaborative thinking, on the basis of building a collaborative model of complex system including economic system innovation, technological innovation and clean government and analysis with Chinese data of 2000-2012 year, we made a regression analysis to the interaction factor of the innovational collaboration of economic system and technology and the comprehensive index of clean government to explore the reasons of coupling relationship change. The results show that Chinese economic system innovation, technological innovation levels are still low, the coupling degree of. clean government and economic system innovation, technological innovation are too low, China needs to actively establish a clean government construction system based on the innovational collaboration of economic system and technology, so that we can realize real long-term and sustainable development of clean government.