The article focuses on the problems in the research administration of Chinese universities, such as the separation of administrative function, the lack of performance evaluation and the lag of process management. By introducing the BPR - Business Process Reengineering - theory, we rethink the Process Reengineering of universities’ research administration from three aspects: administrative ideas, organizational structures and management approaches. Finally, we propose a model of practice based on modern management ideas and information technology, which takes process reengineering as the main body and targets on achieving the vertical (faculty groups) and horizontal (administration department) linkage, to build a new three-dimensional, comprehensive and non-blind-spot network of synergy mechanism in research administration for today’s universities.