Abstract:The future is led by science and technology and the development is driven by innovations. In this sense, scientific and technological innovation carries people's expectations for a better life, and is an important driving force and cornerstone of social progress. In this study, the super-efficiency SBM and Malmquist index model are used to quantitatively explore the efficiency of scientific and technological innovation development in Anhui, Jiangsu, Zhejiang, and Shanghai of Yangtze River Delta from 2012 to 2021. The results showed that:1.the overall level of scientific and technological innovation efficiency is 0.64, which does not reach the efficiency frontier, but the overall trend is on the rise. 2.The comprehensive technical efficiency level of each region is not high and the interregional gap is significant. 3.The average annual growth rate of total factor productivity of scientific and technological innovation is 16.5%, which is biased towards the single-track driving mode of technological progress. Therefore, in order to effectively improve the efficiency of scientific and technological innovation in Yangtze River Delta, it is proposed to optimize the input structure of innovation resources in terms of funds and talent input. Still, as to output, it is suggested to improve government management and promote the industrialization and transformation of scientific and technological achievement. Besides, as for the promotion of regional coordination, it is advised that innovation elements should flow across provinces (cities), and the innovation capability should be enhanced.