With the sustainable development of China's economy，innovation has become the focus of economic development. This paper establishes an input-output index system and uses the Super-Efficience DEA model and Malmquist index model to analyze the science一tethnology resource allocation efficiency of the Yangtze River economic zones on the basis of the dada collected in 11 provinces from 2001 t0 2004. The results show that the allocation capacity of the overall areas is on the rise，but over half of these places are inefficient. Furthermore，This paper provides reasonable support for the decision of the innovation and development of the Yangtze River Economic Zones.