Abstract: Innovation is a pioneer driving force for development, and green development is the primary requirement of the Yangtze River Economic Belt Strategy. Taking 108 cities in Yangtze River Economic Belt as the objects, we construct a comprehensive evaluation system of scientific and technological innovation and green development. Using entropy method, coupling coordination degree model and the spatial Markov chain method, this paper analyzes the coupling degree, spatial-temporal distribution and correlation of scientific and technological innovation and green development in the Yangtze River Economic Belt from 2006 to 2016. The conclusions are as follows. Firstly, during the research period, the scientific and technological innovation and green development index of Yangtze River Economic Belt have generally increased, but the overall level is low which only appear to grow simultaneously after 2013. Secondly, the coupling degree and coordination index of scientific and technological innovation and green development are on an upward trend,while the spatial differentiation within the belt is obvious，and that in the Yangtze River Delta is markedly higher than that of other regions. Thirdly, The coordination of technological innovation and green development is clustered, showing a declining feature of “downstream＞midstream＞upstream”. Cities among lower coordination index can be classified into three types, namely “leading in technology innovation”, “leading in green development” and “balanced”. Besides, there exists significant spatial spillover effects in the coordination of scientific and technological innovation and green development. The transformation of the coordination degree in adjacent cities has similar characteristics. Finally, corresponding policy suggestions are provided.