The construction of regional low carbon innovation system is an effective regional response mechanism to global climate change. Taking the Yangtze RiverEconomic Zone as the research object, this paper discusses the development of the regional low carbon innovation system. Economic development, energy consumption, resource utilization, technological innovation together with carbon emissions and treatment these five aspects are combined to construct an objective and feasible comprehensive evaluation index system of the Yangtze River Economic Zone, and apply BP neural network model for its comprehensive evaluation. The difference among the development of low carbon innovation system in the Yangtze River Economic Zone in 11 provinces and cities is pointed out, and the corresponding countermeasures are put forward.