As an important water source for Guangdong Province and Hong Kong area, Dongjiang River is directly related to the economic development of the Pearl River Delta region and the prosperity and stability of the Hong Kong Special Administrative Region. In order to grasp the development trend of the health status of the Dongjiang River system and promote sustainable development of the economic society in Dongjiang River Basin, regarding to the oscillatory distribution characteristics of Dongjiang River system health scores (2015—2019), a M-DGM(1,1) grey prediction model was constructed based on the grey predicting theory and the gray recurrence dynamic model with equal dimension to assess the future health status of the river system (2020—2024). The results show that the accuracy of the prediction model can reach the first level, and the model can meet the requirements of health assessment of the Dongjiang River system. It is found that the health status of the Dongjiang River system is in the sub-healthy state during 2020—2024, but the overall development is improving towards healthy. The scores of some sensitive warning indices (2020—2024) fluctuated, so it is necessary to strengthen the protection and management of the health of the Dongjiang River system.