At present, the Yangtze River Delta regional integration process presents a deep, multi - field pattern, and the cooperation mechanism is also facing the system, standardization, and the rule of law and the overall development. Under the guidance of the "Yangtze River Delta regional planning", the development of the Yangtze River Delta region is also facing the third transition, and the cooperation mechanism innovation is very important. This paper firstly discusses the significance of 45 period of Yangtze River Delta regional cooperation system and mechanism innovation, followed by the introduction of the historical evolution of the Yangtze River Delta cooperation system and mechanism, and then explain the characteristics of Yangtze River Delta regional cooperation system and mechanism, and then a detailed analysis of the main problems exist in the Yangtze River Delta regional cooperation system and mechanism, and points out countermeasures and suggestions for the innovation of the Yangtze River Delta regional cooperation mechanism. <<