Big data technology is the product of the rapid development of information technology, and various industries such as transportation and e-commerce have paid more attention to the application of information technology. Infiltrating it into scientific research management in universities can promote management innovation. This paper discusses the innovation strategy of scientific research management in universities under the background of big data, specifically analyzes the optimization path of scientific research management under the application of advanced technology and provides reference for scientific research management in universities. At present, universities must not only have strong competitiveness, but also must do a good job in economic management and the analysis of economic activities, to some extent, directly affects the production development and future development direction of colleges and universities. Based on this, the article conducts an in-depth analysis of the innovation of scientific research management in universities under the new situation from multiple angles and levels, to promote scientific research in universities to become an important driving force for modern economic development.