At present, many of China’s S&T innovation input and output indicators rank among the top in the world. In this context, how to objectively measure S&T innovation efficiency and make international comparisons is particularly important. The paper uses the Bootstrap-DEA method to calculate and analyze S&T innovation efficiency in 36 countries, including China, from 2009 to 2018 by establishing S&T innovation input-output indicator system. The paper found that the traditional BCC-DEA model has certain errors in measuring S&T innovation efficiency, and the efficiency value after the Bootstrap method is more reasonable; There are significant differences in S&T innovation efficiency in various countries, especially the internal differentiation of S&T innovation efficiency in innovative countries, The United States, the United Kingdom, Japan, and Germany are significantly ahead of other innovative countries in terms of S&T innovation efficiency; In 2018, China’s S&T innovation efficiency value was 0.848 2, ranking 13th in the world, belonging to the category of high-input and high-efficiency countries; In 2014, China entered the New Normal, the national S&T innovation force layout has significantly promoted the steady improvement of China’s S&T innovation efficiency. The international ranking of S&T innovation efficiency has made steady progress, but it still lags behind the world’s major innovative countries such as the United States, the United Kingdom, and Japan.