Abstract: Innovation is the source of power leading the development. At present, a new round of scientific and technological revolution is ready to take place. China continues to make efforts to speed up catching up and surpassing, and has become a major scientific and technological country with global influence. However, compared with the strategic goals of being among the forefront of innovative countries and the world's scientific and technological power, there is still a big gap in the capabilities and environment of its scientific and technological innovation. The situation that key core technologies are controlled by others has not yet been fundamentally changed. Scientific research cooperation plays an important role in promoting scientific and technological innovation and development. Nowadays, the cooperation rate in the scientific research field is rising. The behavior of scientific researchers and the success of cooperative research are closely related to resources. When faced with a wealth of scientific research cooperation network resources, it is necessary to improve the ability to identify high-quality resources, otherwise it will be like being trapped in "the cave of the silken web". Universities are one of the main bodies of scientific and technological innovation. As a strategic highland for gathering, training and exerting high-level talents, how universities carry out scientific research cooperation is an important topic that is generally concerned by the academic circles. Previous research on the scope of scientific research cooperation and scientific research output has been carried out from three levels: macro level (nation), meso level (institution or field) and micro level (researcher). Much research has focused on the direct relationship between the two, while insufficient attention has been paid to the mediating effect and the moderating effect. This paper focuses on the scientific research cooperation of university scholars at the micro level and takes the research perspective of mediation and moderation as the breakthrough point. Aiming at the relationship between the scope of cooperation and scientific research output, it analyzes the moderating role of three types of network embeddedness (positional embeddedness, relational embeddedness and structural embeddedness) and the mediating role of national funding. Based on the above analysis, a mediated moderation model is constructed. Taking as a sample of 1,292 authors of 4,365 cooperative papers in the category of "Nanoscience & Nanotechnology" in the SCIE of Web of Science from 8 research universities in Shanghai from 2018 to 2020, this paper verifies the model through empirical research. The results show that: (1) International cooperation is more conducive to scholars to improve scientific research output; (2) National funding plays a part of the mediating role between the scope of cooperation and scientific research output; (3) Network embeddedness moderates the relationship between the scope of cooperation and scientific research output. When the network embeddedness of a scholar is at a high level, the influence of the scope of cooperation on scientific research output is strengthened and part of the moderating effect of positional embeddedness and structural embeddedness is achieved through national funding. The construction and testing of the mediated moderation model in this paper expands the research boundary of the relationship between the scope of scientific research cooperation and scientific research output, and also provides new ideas for scientific research cooperation research from the perspective of funding and network embeddedness. This paper presents the influence process of scientific research cooperation on scientific research output more three-dimensionally. This provides more targeted ideas and suggestions for scientific researchers to participate in international cooperation, obtain funding, use scientific research resources more effectively, and support the improvement of their scientific research output. It also provides a reference for universities and related departments in charge of funding to formulate various policies related to scientific research.