Calculate the ecological protection efficiency and the development efficiency of science and technology service industry in 11 provinces of the Yangtze river economic belt from the year 2010 to 2016 by constructing the Super-efficiency DEA model and the method of window analysis. Analyze the influence between them by constructing the model of spatial econometric. The results show that the ecological protection efficiency of 11 provinces along the Yangtze river economic belt is significantly different from the development efficiency of science and technology service industry. The efficiency of scientific research and technological service industry has a positive impact on the efficiency of ecological protection in local and surrounding areas. The efficiency of science and technological capital service industry has a positive effect on the local ecological protection efficiency，but it has a restraining effect on the surrounding area. The scientific and technological publicity service industry has no significant impact on the efficiency of ecological protection. It is suggested to strengthen the construction of local ecological protection science and technology personnel and establish the ecological protection science and technology alliance of the Yangtze river economic belt. Establish a financing mechanism for diversified and market-oriented science and technology capital，and increase the total amount of science and technology capital；we will enrich promotion platforms and make ecological protection science and technology more specialized.