Using the upper and middle reaches of the Heilongjiang River as an example, we assessed the health status of international boundary rivers in this study. In order to comprehensively analyze the randomness and fuzziness during the assessment, we introduced the cloud model into the study and constructed a river health assessment system for the upper and middle reaches of the Heilongjiang River. The criterion layer of the system contained seven factors, including river hydrology, river morphology, and characteristics of water, and the index layer of the system contained 16 indices. The system was used to assess the river health in the typical year of 2013. The results show that the river health was at the middle level in 2013. We also analyzed the main factors that affected the river health and put forward a series of measures for river management improvement, including enhancement of water pollution control, reinforcement of dams along the river bank, reforestation of cultivated land and restoration of wetlands, and implementation of ecological operation.