Recent studies shed light on the key elements that influence the link among research funds, collaborative activities and scientific outputs. However, most researches focused on the effects of research fund, and cooperation was only considered as an independent determinant of research productivity. In this paper we evaluate the mediating role of cooperation in the relationship between research fund and scientific outputs of individuals. We conduct a multiple linear regression study to NSFC-Guangdong Joint Fund. Leveraging 40 interviews to the correlated scientists of NSFC-Guangdong Joint Fund, 16 interviews to research directors from universities, and 12 interviews to program managers in the government of Guangdong Province, we examine how NSFC-Guangdong Joint Fund may affects the scientific outputs of individuals in Guangdong through promoting their cross-regional cooperation. Then, we estimate this effect using Web of Science database and our own application database, and find cross-regional cooperation plays a mediating role in prompting the interaction between the fund and scientific outputs of individuals in Guangdong Province.