This article aims to explore the influence of Mainland China's inter-governmental relations to the logistics in the Yangtze River Delta region. In short, research results can be summed up and related to Yangtze River Delta regions relationship between inter-structural governmental factors, to allow readers to understand the status of the logistics industry and policy development in the Yangtze River Delta and it¡¦s obstacles. Through governmental inter-system structure, relating to the Yangtze River Delta region's logistics industry environment review, analysis between local government in Yangtze River Delta, and the existence of competitive behavior, different difficulties, as well as logistics management system of the Government; on the other hand, Central Government policies on logistics development in Yangtze River Delta region and the role it plays, furthermore what means of intervention is necessary. Finally we can conclude that, Under the influence of inter-institutional structure, logistics reforms in the management of the local government and functions of the Central Government policies have been meet with difficulty; on the other hand, tax reform in logistics by means of Central Government macro-control, yet still compressed direct access to tax revenue of the local governments financial capacity, resulting in local governments to rely more on other non-tax revenues, indirect effects of layouts and the operation of the logistics industry chain. Due to these structural factors that affect local government in Yangtze River Delta areas causes a dilemma in choosing to compete or cooperate; reflecting to the effectiveness of the reform policies of the Central Government.