The data‐based institutional research has been gradually adopted by more and more universities around the world. To develop the institutional research and solve the management problems of universities, the construction of institutional research data system has been put forward to be more intelligent, more accurate, more stable and more efficient. This paper analyzes the difficulties and challenges encountered in the construction of intelligent data system in colleges and universities, puts forward a new two‐level model of university and college to promote the effectiveness of construction, and gives suggestions from three aspects of institutional improvement, platform construction and researcher training, to provide useful ideas for the universities.