Abstract： The State Key Specialized Scientific Projects bring the unprecedented opportunity for the development of variety disciplines and provide the critical timing for the improvement of science and technology of university. Meanwhile, it presents new challenges to develop the frontier of sciences and to promote cooperation and cross of different disciplines. Through the process of the programs, we will expect to train and find team leaders and outstanding scientists. This paper presented the brief outline how the researchers from the Departments of Infectious Disease and School of Pharmacy in Fudan University collaborated in a cross-discipline manner and integrated the research resources based on the objectives of the research programs. During the application, they reorganized research teams, combined the overlapping research fields to focus the direction of research fields according to the national and research needs. In the process of their application, they finally promoted the capacities for their competition and innovation which were undoubted to help us to establish headship/main forces in the fields of infectious disease precaution and devolvement of new clinical medicine in the future.