Synergy innovation is not only the inherent demand for the transition of regional development stages，but also the inevitable choice to follow the law of development and catch up with the frontiers of the world. This report designs the Yangtze River Delta Synergy Innovation index system based on five aspects：resource sharing，innovation cooperating，achievement sharing，industrial linking and environmental supporting. The work help to monitors and evaluates the synergy innovation of Shanghai and other three provinces in the Yangtze River Delta through detailed data processing and new perspective of analysis methods，containing the main characteristics，dynamic trends and weak links of innovation. Last，the article put forward rational development suggestions in order to supporting Synergy Innovation on the strategy aspects.