Starting from the introduction of the management of scientific research project, and then gives a detailed description based on J2EE architecture, the lightweight composite framework involving Spring, Struts and iBATIS and an iterative method is employed in project management. With a series of functions such as application, recommendation, processing, approval, assessment and management of scientific research project and so on, the system has the characteristics of easy maintenance, dynamic propagation and strong expansibility. Finally the safety of the system is discussed from two perspectives, namely its design and environment. Years’ of application in the management of scientific research project in Gansu Province has proved its good stability, fast response and high safety.