Abstract: The new rural construction in China faces the increasing pressure from the conflict between economic development and environment protection. It is the important task to build the collaborative mechanism between environment protection and economic development not only for China’s new rural construction but also for the national construction of ecological civilization. Based on the multidisciplinary sight of Synergetic, system theory, and environmental economics, this paper analyzed the collaborative subject and function of economic development and environment protection and built five interdependent mechanism systems: 1) the two-way feedback regulatory mechanism between environmental priorities synergistic goals and a comprehensive system of collaborative measure; 2) the synergy mechanism among government guidance, enterprise-led, farmer participated social service organizations; 3) the coordinative mechanism between different subjects and regions based on the core interests of ecological compensation; 4) the interactive mechanism among rural urbanization, key areas, key industries and the rural space; and 5) the organization and management mechanism which is to achieve the synergy targets, collaborative tools and to promote the collaborative and cooperative areas of the subject. For the new rural construction, results indicated that cooperation mechanism between economic development and environment protection had multidimensional theory and practice which can achieve the comprehensive, dynamic, and orderly synergy between economic development and environmental protection.