Urban rivers, located in the strong interaction area of human activities and natural processes, are under great pressure of human resource development and utilization and pollutant discharge. In recent years, people have adopted a series of management measures to improve the health of urban rivers. However, current methods about urban river health assessment mainly focus on the pressures from human activities. The positive measures taken by humans to restore the ecology of urban rivers are usually neglected. Thus, the assessment results cannot fully reflect the real river health state and may mislead the management and protection of urban rivers. Therefore, both of the negative and positive human activities should be considered when constructing the assessment index system of urban river health, which can provide a more scientific and accurate assessment result. In this study, a typical urban river (the Northwest-Moat) in Nanjing City was selected as the study area. Considering the spatial heterogeneity of river health, we divided the Northwest-Moat into six reaches according to the river's surrounding architecture environment, its morphological characteristics and distribution of urban pipe network. A pressure-state-response (PSR) model was then proposed to construct the health index system with the consideration of human restoration measures on river health. The matter-element extension model was used to determine the final grade of each river reach and judge the development trend of each river reach's health. The results showed that the weights of pressure, state and response criterion layer were 0.458, 0.311 and 0.231 respectively. The pressure indices were the main impact factors of river health, when compared to the state indices and response indices. The health levels of six river sections showed great spatial heterogeneity, and the health grades from reach A to reach F were moderate, health, sub-health, moderate, sub-illness and illness respectively. The health grades of the river reaches that run through parks were significantly higher than those run through residential areas. The health level of reach B, reach C and reach D has a tendency for further improvement, while the health status of reach A, reach E and reach F has a tendency for further deterioration. Therefore, more attentions should be paid to the reach A, reach E and reach F to improve their health status in future studies. Overall, the proposed method in the study, which combined PSR model and matter-element extension model, could effectively assess the ecosystem health status and change trend of urban rivers and would provide scientific guidance for future ecological restoration.