The DEA-BCC method and Malmquist index model are used to measure and analyze the changes of scientific and technological innovation efficiency in industry in 11 provinces and cities of the Yangtze River Economic Belt from 2006 to 2017. The results show that: During this period, the overall scientific and technological innovation efficiency in industry of the Yangtze River Economic Belt has been significantly improved, great progress has been made in the technical level and management level, and the scale investment has brought about the efficiency improvement. The difference of scientific and technological innovation efficiency in industry between provinces and cities in the Yangtze River Economic Belt decreases year by year, and theprovinces and cities with weak foundation of scientific and technological innovation show strong posterior advantages, and the level of scientific and technological innovation has obviously improved.