The interconnected river system network (IRSN), as an important strategy of national water security, is actively promoted in China. There are great significances to improve the ability of water resources allocation, guarantee river and lake health, and control floods and droughts. A large number of IRSN practical projects have been built to bring huge benefits, but they are facing risks such as ecologic and environmental deteoriation, water shortage and economic loss. Therefore, we need theoretical systems as the guidance to achieve more eco-economic comprehensive benefits from IRSN in the future. However, the theories of IRSN, are just rare and fractional, far from a complete system. It is urgent to promote the theoretical construction based on the relevant scientific theories. This paper firstly discussed the systemic and interdisciplinary characteristics of the theories of IRSN, and then analyzed the relationship between the IRSN theories and some main relevant scientific theories including the sustainable development theory, hydrology theories, hydrodynamics theories, economics theories, ecological theory and system science theory, which were thought to helpfully provide the valuable theoretical basis for IRSN. The IRSN theories system should be built and innovated on the basis of the comprehensive systems of these relevant scientific theories. Considering the urgent demands for the operation of IRSN, the theory research in some priority areas should been done, such as the theory and methods of the IRSN connectivity and function assessment, the theory of the IRSN coupling mechanism and system stability, the theory of the IRSN compatibility, the theory of matching of the IRSN and economic pattern, the theory of the IRSN impact mechanism and evaluation on ecological environment, the theory of the uncertainty and adaptability of IRSN giant systems. All these theories and some priority areas of the IRSN theory systems would provide a strong support for the IRSN projects implementation and benefits.