As the core growth pole of Hunan economy and society of important support of building urban agglomerations in the middle reaches of the Yangtze River in new era，the development of Changsha-Zhuzhou-Xiangtan urban agglomeration has entered a new era of taking the lead from overall well-off to the basic realization of modernization，and the integration of Changsha-Zhuzhou-Xiangtan urban agglomeration also has achieved great achievements in the past thirty-six years. However, in the process of integrated development of Changsha-Zhuzhou-Xiangtan urban agglomeration, there are also practical problems such as difficult planning, lack of power, monopolization of one city, simple administration, and overall marketization. After the creation and introduction of the polycentric network governance synergistics theory，this paper constructs the model of polycentric network governance synergistic on the integration of Changsha-Zhuzhou-Xiangtan urban agglomeration，and puts forward the innovation countermeasure of the system mechanism of obstruction，including six aspects: constructing and implementing joint law enforcement mechanism based on rigidity of constraint; establishing and perfecting overall coordinating mechanism based on optimization of the whole; establishing universal sharing mechanism based on diversity of subject; establishing and perfecting the mechanism of resource sharing based on elasticity of guidance; perfecting policy synergy mechanism based on diversification of the function; establishing and improving performance evaluation mechanism based on co-responsibility of risk.