Seven megacities along the Yangtze River Economic Belt，such as Chongqing，Shanghai，Chengdu，Suzhou，Wuhan，Hangzhou and Nanjing，are selected as research objects. From four dimensions：the scale of industrial development，the level of industrial innovation，the level of industrial green development and industrial service development，the report establishes the evaluation index system of industrial development level，and compares industrial development level of the seven cities. The report chooses DEA-Malmquist index to measure the efficiency of industrial innovation for the seven megacities. The results show that：there are large significant differences in the level of industrial development of the megacities in Yangtze River Economic Belt；the efficiency of industrial innovation is closely related to the stage of industrial development，the relationship is roughly “N” gradient distribution. If we want to promote the industrial of the megacities in the Yangtze River Economic Belt develop sustainedly and healthily，we should pay attention to enhance the development of quality，improve the ability of independent innovation，strengthen energy conservation，promote the integration of industry and service.