International cooperations have played an important role in academic activities as more and more researchers endeavor to participate in joint research or exchange with partners aboard. Focused on projects of Major International (Regional) Joint Research Program of the Natural Science Foundation of China (NSFC) from 2003 to 2008, we have investigated the characteristics of the scientific cooperation by mapping the funded projects from the aspects of topics, affiliations and cooperative countries (regions), respectively. Moreover, it is demonstrated that issues related to nano technologies, genes and ecological environments have become the hot topics in the joint research of NSFC, and projects with issues of big science have been preferentially funded under the program's guide posted every year. Moreover, most granted projects were undertaken by the minority of affiliations ith the leading research capability, which is the same to partners abroad. The aggregation effect has been greatly improved with the bilateral or multilateral agreement signed with scientific organizations abroad, so has the competitive mechanism of scientific resources allocation.