Abstract: Comprehensively promoting rural revitalization has entered a critical stage. Because of the long-term dual structure between urban and rural areas, the gap between urban and rural areas is significant, and the rural market is not mature. System breakthrough and innovation are the first hand of urban-rural integration and rural revitalization. In order to fully explore the key system problems in the revitalization of rural areas in China, this study takes Weifang City in Shandong Province as an example, selects 23 research points to carry out in-depth research, analysis and research, and explores the key problems in rural revitalization of Weifang and puts forward corresponding institutional innovation measures. At present, Weifang has achieved initial results in agricultural industry, but it lacks institutional innovation in many common problems such as poor circulation of rural asset, single financing mode, too large gap between urban and rural areas, low level of grass-roots governance, lack of policy mechanism of introducing wisdom into village and so on. In order to promote the rural revitalization of Weifang City in an all-round way, this paper puts forward specific innovation measures in the aspects of property rights system, industrial structure and economic organization, social structure and mechanism governance, which provides important basis for guiding the rural revitalization of Weifang City. At the same time, it provides important reference for promoting the institutional reform of rural revitalization in China.