As river basin with unique spatial attributes and regional functions, it continues to vigorously promote economic development. However, the study of river basin economic theory in the new era is relatively weak, and it is difficult to organically combine Marxist river basin economic thought with the practice of China’s river basin economic development. This paper systematically combs the relevant literature at home and abroad, guided by the important scientific issues in the development of China’s river basin economic theory in the new era, and based on the academic chain of “connotation characteristics-practical performance-core theory-methodology system”, constructs the framework of China’s river basin economic theory system in the new era. This paper successively explains the connotation, main characteristics, realistic performance, core theory and research method system of China’s river basin economy in the new era in the theoretical framework. This paper discusses the expansion of the theoretical system of China’s river basin economy in the new era and the future research direction from three aspects: the in-depth study of the theoretical system of China’s river basin economy in the new era, the guidance of the concept of China’s river basin economic development in the new era, and the construction of an original river basin economic theory combined with China’s situation.